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Baramee S, Thianheng P, Uke A, Cheawchanlertfa P, Tachaapaikoon C, Waeonukul R, Pason P, Ratanakhanokchai K, Liu YJ, Kosugi A. Extracytoplasmic polysaccharides control cellulosomal and non-cellulosomal systems in Herbivorax saccincola A7. Appl Microbiol Biotechnol 2024; 108:477. [PMID: 39352555 PMCID: PMC11445354 DOI: 10.1007/s00253-024-13310-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2024] [Revised: 09/09/2024] [Accepted: 09/10/2024] [Indexed: 10/04/2024]
Abstract
Herbivorax saccincola A7 is an anaerobic alkali-thermophilic lignocellulolytic bacterium that possesses a cellulosome and high xylan degradation ability. To understand the expression profile of extracellular enzymes by carbon sources, quantitative real-time PCR was performed on all cellulosomal and non-cellulosomal enzyme genes of H. saccincola A7 using cellulose and xylan as carbon sources. The results confirmed that the scaffolding proteins of H. saccincola A7 were expressed. In general, the cellulosomal genes belonging to the glycoside hydrolase families 9, 10, 11, and 48 were repressed when xylan was the sole carbon source, but these genes were significantly induced in the presence of cellulose. These results indicate that cellulose, not xylan, is a key inducer of cellulosomal genes in H. saccincola A7. The RsgI-like proteins, which regulate a carbohydrate-sensing mechanism in Clostridium thermocellum, were also found to be encoded in the H. saccincola A7 genome. To confirm the regulation by RsgI-like proteins, the relative expression of σI1-σI4 factors was analyzed on both carbon sources. The expression of alternative σI1 and σI2 factors was enhanced by the presence of cellulose. By contrast, the expression of σI3 and σI4 factors was activated by both cellulose and xylan. Taken together, the results reveal that the cellulosomal and non-cellulosomal genes of H. saccincola A7 are regulated through a carbohydrate-sensing mechanism involving anti-σ regulator RsgI-like proteins. KEY POINTS: • qRT-PCR performed on cellulosomal and non-cellulosomal genes of H. saccincola A7 • Cellulose is a key inducer of the cellulosome of H. saccincola A7 • H. saccincola A7 possesses a similar system of anti-σ regulator RsgI-like proteins.
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Affiliation(s)
- Sirilak Baramee
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki, 305-8686, Japan
- Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Bangkok, 10150, Thailand
| | - Pakinee Thianheng
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki, 305-8686, Japan
- Enzyme Technology Laboratory, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok, 10150, Thailand
| | - Ayaka Uke
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki, 305-8686, Japan
| | - Pattsarun Cheawchanlertfa
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki, 305-8686, Japan
- Enzyme Technology Laboratory, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok, 10150, Thailand
| | - Chakrit Tachaapaikoon
- Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Bangkok, 10150, Thailand
- Enzyme Technology Laboratory, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok, 10150, Thailand
| | - Rattiya Waeonukul
- Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Bangkok, 10150, Thailand
- Enzyme Technology Laboratory, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok, 10150, Thailand
| | - Patthra Pason
- Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Bangkok, 10150, Thailand
- Enzyme Technology Laboratory, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok, 10150, Thailand
| | - Khanok Ratanakhanokchai
- Enzyme Technology Laboratory, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok, 10150, Thailand
| | - Ya-Jun Liu
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Shandong Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, PR China
- Shandong Energy Institute, Qingdao, 266101, PR China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, PR China
| | - Akihiko Kosugi
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki, 305-8686, Japan.
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Kuga T, Sunagawa N, Igarashi K. Effect of Free Cysteine Residues to Serine Mutation on Cellodextrin Phosphorylase. J Appl Glycosci (1999) 2024; 71:37-46. [PMID: 38863949 PMCID: PMC11163329 DOI: 10.5458/jag.jag.jag-2023_0011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 01/19/2024] [Indexed: 06/13/2024] Open
Abstract
Cellodextrin phosphorylase (CDP) plays a key role in energy-efficient cellulose metabolism of anaerobic bacteria by catalyzing phosphorolysis of cellodextrin to produce cellobiose and glucose 1-phosphate, which can be utilized for glycolysis without consumption of additional ATP. As the enzymatic phosphorolysis reaction is reversible, CDP is also employed to produce cellulosic materials in vitro. However, the enzyme is rapidly inactivated by oxidation, which hinders in vitro utilization in aerobic environments. It has been suggested that the cysteine residues of CDP, which do not form disulfide bonds, are responsible for the loss of activity, and the aim of the present work was to test this idea. For this purpose, we replaced all 11 free cysteine residues of CDP from Acetivibrio thermocellus (formerly known as Clostridium thermocellum) with serine, which structurally resembles cysteine in our previous work. Herein, we show that the resulting CDP variant, named CDP-CS, has comparable activity to the wild-type enzyme, but shows increased stability to oxidation during long-term storage. X-Ray crystallography indicated that the mutations did not markedly alter the overall structure of the enzyme. Ensemble refinement of the crystal structures of CDP and CDP-CS indicated that the C372S and C625S mutations reduce structural fluctuations in the protein main chain, which may contribute to the increased stability of CDP-CS to oxidation.
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Affiliation(s)
- Tomohiro Kuga
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | - Naoki Sunagawa
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | - Kiyohiko Igarashi
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo
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Chen C, Yang H, Dong S, You C, Moraïs S, Bayer EA, Liu Y, Xuan J, Cui Q, Mizrahi I, Feng Y. A cellulosomal double-dockerin module from Clostridium thermocellum shows distinct structural and cohesin-binding features. Protein Sci 2024; 33:e4937. [PMID: 38501488 PMCID: PMC10949318 DOI: 10.1002/pro.4937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/05/2024] [Accepted: 02/07/2024] [Indexed: 03/20/2024]
Abstract
Cellulosomes are intricate cellulose-degrading multi-enzymatic complexes produced by anaerobic bacteria, which are valuable for bioenergy development and biotechnology. Cellulosome assembly relies on the selective interaction between cohesin modules in structural scaffolding proteins (scaffoldins) and dockerin modules in enzymes. Although the number of tandem cohesins in the scaffoldins is believed to determine the complexity of the cellulosomes, tandem dockerins also exist, albeit very rare, in some cellulosomal components whose assembly and functional roles are currently unclear. In this study, we characterized the structure and mode of assembly of a tandem bimodular double-dockerin, which is connected to a putative S8 protease in the cellulosome-producing bacterium, Clostridium thermocellum. Crystal and NMR structures of the double-dockerin revealed two typical type I dockerin folds with significant interactions between them. Interaction analysis by isothermal titration calorimetry and NMR titration experiments revealed that the double-dockerin displays a preference for binding to the cell-wall anchoring scaffoldin ScaD through the first dockerin with a canonical dual-binding mode, while the second dockerin module was unable to bind to any of the tested cohesins. Surprisingly, the double-dockerin showed a much higher affinity to a cohesin from the CipC scaffoldin of Clostridium cellulolyticum than to the resident cohesins from C. thermocellum. These results contribute valuable insights into the structure and assembly of the double-dockerin module, and provide the basis for further functional studies on multiple-dockerin modules and cellulosomal proteases, thus highlighting the complexity and diversity of cellulosomal components.
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Affiliation(s)
- Chao Chen
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic BiologyQingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdaoChina
- Shandong Energy InstituteQingdaoChina
- Qingdao New Energy Shandong LaboratoryQingdaoChina
- University of Chinese Academy of SciencesBeijingChina
| | - Hongwu Yang
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic BiologyQingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdaoChina
- Present address:
College of PharmacyNankai University, Tongyan Road 38, Haihe Education Park, Jinnan DistrictTianjin 300350China
| | - Sheng Dong
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic BiologyQingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdaoChina
- Shandong Energy InstituteQingdaoChina
- Qingdao New Energy Shandong LaboratoryQingdaoChina
- University of Chinese Academy of SciencesBeijingChina
| | - Cai You
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic BiologyQingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdaoChina
- Shandong Energy InstituteQingdaoChina
- Qingdao New Energy Shandong LaboratoryQingdaoChina
| | - Sarah Moraïs
- Department of Life Sciences and the National Institute for Biotechnology in the NegevBen‐Gurion University of the NegevBeer‐ShevaIsrael
| | - Edward A. Bayer
- Department of Life Sciences and the National Institute for Biotechnology in the NegevBen‐Gurion University of the NegevBeer‐ShevaIsrael
- Department of Biomolecular SciencesThe Weizmann Institute of ScienceRehovotIsrael
| | - Ya‐Jun Liu
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic BiologyQingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdaoChina
- Shandong Energy InstituteQingdaoChina
- Qingdao New Energy Shandong LaboratoryQingdaoChina
- University of Chinese Academy of SciencesBeijingChina
| | - Jinsong Xuan
- Department of Biological Science and Engineering, School of Chemical and Biological EngineeringUniversity of Science and Technology BeijingBeijingChina
| | - Qiu Cui
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic BiologyQingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdaoChina
- Shandong Energy InstituteQingdaoChina
- Qingdao New Energy Shandong LaboratoryQingdaoChina
- University of Chinese Academy of SciencesBeijingChina
- State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoChina
| | - Itzhak Mizrahi
- Department of Life Sciences and the National Institute for Biotechnology in the NegevBen‐Gurion University of the NegevBeer‐ShevaIsrael
| | - Yingang Feng
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic BiologyQingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdaoChina
- Shandong Energy InstituteQingdaoChina
- Qingdao New Energy Shandong LaboratoryQingdaoChina
- University of Chinese Academy of SciencesBeijingChina
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Xiao Y, Dong S, Liu YJ, You C, Feng Y, Cui Q. Key roles of β-glucosidase BglA for the catabolism of both laminaribiose and cellobiose in the lignocellulolytic bacterium Clostridium thermocellum. Int J Biol Macromol 2023; 250:126226. [PMID: 37558019 DOI: 10.1016/j.ijbiomac.2023.126226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 07/31/2023] [Accepted: 08/06/2023] [Indexed: 08/11/2023]
Abstract
The thermophilic bacterium Clostridium thermocellum efficiently degrades polysaccharides into oligosaccharides. The metabolism of β-1,4-linked cello-oligosaccharides is initiated by three enzymes, i.e., the cellodextrin phosphorylase (Cdp), the cellobiose phosphorylase (Cbp), and the β-glucosidase A (BglA), in C. thermocellum. In comparison, how the oligosaccharides containing other kinds of linkage are utilized is rarely understood. In this study, we found that BglA could hydrolyze the β-1,3-disaccharide laminaribiose with much higher activity than that against the β-1,4-disaccharide cellobiose. The structural basis of the substrate specificity was analyzed by crystal structure determination and molecular docking. Genetic deletions of BglA and Cbp, respectively, and enzymatic analysis of cell extracts demonstrated that BglA is the key enzyme responsible for laminaribiose metabolism. Furthermore, the deletion of BglA can suppress the expression of Cbp and the deletion of Cbp can up-regulate the expression of BglA, indicating that BglA and Cbp have cross-regulation and BglA is also critical for cellobiose metabolism. These insights pave the way for both a fundamental understanding of metabolism and regulation in C. thermocellum and emphasize the importance of the degradation and utilization of polysaccharides containing β-1,3-linked glycosidic bonds in lignocellulose biorefinery.
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Affiliation(s)
- Yan Xiao
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Shandong Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China; Dalian National Laboratory for Clean Energy, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China
| | - Sheng Dong
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Shandong Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China; Dalian National Laboratory for Clean Energy, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China
| | - Ya-Jun Liu
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Shandong Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China; Dalian National Laboratory for Clean Energy, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China
| | - Chun You
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Yingang Feng
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Shandong Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China; Dalian National Laboratory for Clean Energy, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China.
| | - Qiu Cui
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Shandong Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China; Dalian National Laboratory for Clean Energy, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China.
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5
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de Camargo BR, Steindorff AS, da Silva LA, de Oliveira AS, Hamann PRV, Noronha EF. Expression profiling of Clostridium thermocellum B8 during the deconstruction of sugarcane bagasse and straw. World J Microbiol Biotechnol 2023; 39:105. [PMID: 36840776 DOI: 10.1007/s11274-023-03546-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 02/10/2023] [Indexed: 02/26/2023]
Abstract
The gram-positive bacterium Clostridium thermocellum contains a set of carbohydrate-active enzymes that can potentially be employed to generate high-value-added products from lignocellulose. In this study, the gene expression profiling of C. thermocellum B8 was provided during growth in the presence of sugarcane bagasse and straw as a carbon source in comparison to growth using microcrystalline cellulose. A total of 625 and 509 genes were up-regulated for growth in the presence of bagasse and straw, respectively. These genes were mainly grouped into carbohydrate-active enzymes (CAZymes), cell motility, chemotaxis, quorum sensing pathway and expression control of glycoside hydrolases. These results show that type of carbon source modulates the gene expression profiling of carbohydrate-active enzymes. In addition, highlight the importance of cell motility, attachment to the substrate and communication in deconstructing complex substrates. This present work may contribute to the development of enzymatic cocktails and industrial strains for biorefineries based on sugarcane residues as feedstock.
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Affiliation(s)
- Brenda Rabello de Camargo
- Laboratory of Enzymology, Department of Cell Biology, University of Brasília, Brasilia, DF, 70910-900, Brazil
| | | | - Leonardo Assis da Silva
- Laboratory of Virology, Department of Cell Biology, University of Brasília, Brasília, DF, Brazil
| | - Athos Silva de Oliveira
- Laboratory of Virology, Department of Cell Biology, University of Brasília, Brasília, DF, Brazil
| | - Pedro Ricardo Vieira Hamann
- São Carlos Institute of Physics, University of São Paulo, Avenida Trabalhador São-Carlense,400, Parque Arnold Schimidt, São Carlos, SP, 13566-590, Brazil
| | - Eliane Ferreira Noronha
- Laboratory of Enzymology, Department of Cell Biology, University of Brasília, Brasilia, DF, 70910-900, Brazil.
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Zhu X, Zhou Z, Guo G, Li J, Yan H, Li F. Proteomics and metabolomics analysis of the lignin degradation mechanism of lignin-degrading fungus Aspergillus fumigatus G-13. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:1062-1076. [PMID: 36723181 DOI: 10.1039/d2ay01446g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Aspergillus fumigatus has the potential to degrade lignocellulosic biomass, but the degradation mechanism is not clear. The purpose of this study is to analyze the differential proteins and metabolites produced by Aspergillus fumigatus G-13 in the degradation of different lignin model compounds. Ferulic acid, sinapic acid, and p-coumaric acid were used as carbon sources. By controlling the culture conditions, and adding a cellulose co-substrate and an auxiliary carbon source, the enzymatic production law of three lignin model compounds degraded by Aspergillus fumigatus G-13 was investigated. Proteomics and metabolomics analysis were conducted for the two groups with the largest difference in enzyme activity expression. The results showed that a total of 1447 peptides were identified by proteomics analysis. Among them, 134 proteins were significantly changed, 73 proteins were up-regulated, and 61 proteins were down-regulated. The key proteins that degrade lignin model compounds are catechol dioxygenase, glutathione reductase, dextranase, isoamyl alcohol oxidase, glyceraldehyde-3-phosphate dehydrogenase and superoxide dismutase. Enrichment analysis of differential metabolite functions revealed that Aspergillus fumigatus G-13 is associated with several pathways related to the degradation of lignin. Among them, starch and sucrose metabolism, pentose phosphate pathway, glutathione metabolism, and the ortho-cleavage pathway of dihydroxylated aromatic rings are closely related to lignin degradation. The information presented in this paper will be helpful for future research on the degradation or depolymerization of natural lignocellulosic substrates.
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Affiliation(s)
- Xudong Zhu
- Heilongjiang Provincial Key Laboratory of CO2 Resource Utilization and Energy Catalytic Materials, China
- School of Material Science and Chemical Engineering, Harbin University of Science and Technology, No. 4, Linyuan Road, Harbin 150040, P. R. China
| | - Zijing Zhou
- Heilongjiang Provincial Key Laboratory of CO2 Resource Utilization and Energy Catalytic Materials, China
- School of Material Science and Chemical Engineering, Harbin University of Science and Technology, No. 4, Linyuan Road, Harbin 150040, P. R. China
| | - Gaijuan Guo
- Heilongjiang Provincial Key Laboratory of CO2 Resource Utilization and Energy Catalytic Materials, China
- School of Material Science and Chemical Engineering, Harbin University of Science and Technology, No. 4, Linyuan Road, Harbin 150040, P. R. China
| | - Jinda Li
- Heilongjiang Provincial Key Laboratory of CO2 Resource Utilization and Energy Catalytic Materials, China
- School of Material Science and Chemical Engineering, Harbin University of Science and Technology, No. 4, Linyuan Road, Harbin 150040, P. R. China
| | - Hong Yan
- Heilongjiang Provincial Key Laboratory of CO2 Resource Utilization and Energy Catalytic Materials, China
- School of Material Science and Chemical Engineering, Harbin University of Science and Technology, No. 4, Linyuan Road, Harbin 150040, P. R. China
| | - Fen Li
- Heilongjiang Provincial Key Laboratory of CO2 Resource Utilization and Energy Catalytic Materials, China
- School of Material Science and Chemical Engineering, Harbin University of Science and Technology, No. 4, Linyuan Road, Harbin 150040, P. R. China
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Moraïs S, Stern J, Artzi L, Fontes CMGA, Bayer EA, Mizrahi I. Carbohydrate Depolymerization by Intricate Cellulosomal Systems. Methods Mol Biol 2023; 2657:53-77. [PMID: 37149522 DOI: 10.1007/978-1-0716-3151-5_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Cellulosomes are multi-enzymatic nanomachines that have been fine-tuned through evolution to efficiently deconstruct plant biomass. Integration of cellulosomal components occurs via highly ordered protein-protein interactions between the various enzyme-borne dockerin modules and the multiple copies of the cohesin modules located on the scaffoldin subunit. Recently, designer cellulosome technology was established to provide insights into the architectural role of catalytic (enzymatic) and structural (scaffoldin) cellulosomal constituents for the efficient degradation of plant cell wall polysaccharides. Owing to advances in genomics and proteomics, highly structured cellulosome complexes have recently been unraveled, and the information gained has inspired the development of designer-cellulosome technology to new levels of complex organization. These higher-order designer cellulosomes have in turn fostered our capacity to enhance the catalytic potential of artificial cellulolytic complexes. In this chapter, methods to produce and employ such intricate cellulosomal complexes are reported.
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Affiliation(s)
- Sarah Moraïs
- Faculty of Natural Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Johanna Stern
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Lior Artzi
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | | | - Edward A Bayer
- Faculty of Natural Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel.
| | - Itzhak Mizrahi
- Faculty of Natural Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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Deciphering Cellodextrin and Glucose Uptake in Clostridium thermocellum. mBio 2022; 13:e0147622. [PMID: 36069444 PMCID: PMC9601137 DOI: 10.1128/mbio.01476-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Sugar uptake is of great significance in industrially relevant microorganisms. Clostridium thermocellum has extensive potential in lignocellulose biorefineries as an environmentally prominent, thermophilic, cellulolytic bacterium. The bacterium employs five putative ATP-binding cassette transporters which purportedly take up cellulose hydrolysates. Here, we first applied combined genetic manipulations and biophysical titration experiments to decipher the key glucose and cellodextrin transporters. In vivo gene inactivation of each transporter and in vitro calorimetric and nuclear magnetic resonance (NMR) titration of each putative sugar-binding protein with various saccharides supported the conclusion that only transporters A and B play the roles of glucose and cellodextrin transport, respectively. To gain insight into the structural mechanism of the transporter specificities, 11 crystal structures, both alone and in complex with appropriate saccharides, were solved for all 5 putative sugar-binding proteins, thus providing detailed specific interactions between the proteins and the corresponding saccharides. Considering the importance of transporter B as the major cellodextrin transporter, we further identified its cryptic, hitherto unknown ATPase-encoding gene as clo1313_2554, which is located outside the transporter B gene cluster. The crystal structure of the ATPase was solved, showing that it represents a typical nucleotide-binding domain of the ATP-binding cassette (ABC) transporter. Moreover, we determined that the inducing effect of cellobiose (G2) and cellulose on cellulosome production could be eliminated by deletion of transporter B genes, suggesting the coupling of sugar transport and regulation of cellulosome components. This study provides key basic information on the sugar uptake mechanism of C. thermocellum and will promote rational engineering of the bacterium for industrial application.
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Zhu L, Li L, Yang Q, Chen L, Zhang L, Zhang G, Lin B, Tang J, Zhang Z, Chen S. Study on microbial community of "green-covering" Tuqu and the effect of fortified autochthonous Monascus purpureus on the flavor components of light-aroma-type Baijiu. Front Microbiol 2022; 13:973616. [PMID: 36060768 PMCID: PMC9434108 DOI: 10.3389/fmicb.2022.973616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 08/01/2022] [Indexed: 11/13/2022] Open
Abstract
"Green-covering" Tuqu (TQ), as one of Xiaoqu, is a special fermentative starter (also known as Jiuqu in Chinese) that originated in southern China and is characterized by a layer of green mold covering (Aspergillus clavatus) the surface and (sometimes) with a red heart. It plays a vital role in producing light-aroma-type Baijiu (LATB). However, to date, the microbiota that causes red heart of TQ remain largely unexplored, and it is still unclear how these microbiota influence on the quality of LATB. In this study, two types of TQ, one with a red heart (RH) and another with a non-red heart (NRH), were investigated by high throughput sequencing (HTS) and directional screening of culture-dependent methods. The obtained results revealed the differences in the microbial communities of different TQ and led to the isolation of two species of Monascus. Interestingly, the results of high performance liquid chromatography (HPLC) detection showed that citrinin was not detected, indicating that Monascus isolated from TQ was no safety risk, and the contents of gamma-aminobutyric acid in the fermented grains of RH were higher than that of NRH during the fermentation. Selecting the superior autochthonous Monascus (M1) isolated from the TQ to reinoculate into the TQ-making process, established a stable method for producing the experimental "red heart" Tuqu (ERH), which confirmed that the cause of "red heart" was the growth of Monascus strains. After the lab-scale production test, ERH increased ethyl ester production and reduced higher alcohols production. In addition, Monascus had an inhibitory effect on the growth of Saccharomyces and Aspergillus. This study provides the safe, health-beneficial, and superior fermentation strains and strategies for improving the quality of TQ and LATB.
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Affiliation(s)
- Liping Zhu
- Hubei Key Laboratory of Quality and Safety of Traditional Chinese Medicine and Health Food, Jing Brand Co. Ltd, Daye, China
| | - Lanqi Li
- Hubei Key Laboratory of Quality and Safety of Traditional Chinese Medicine and Health Food, Jing Brand Co. Ltd, Daye, China
| | - Qiang Yang
- Hubei Key Laboratory of Quality and Safety of Traditional Chinese Medicine and Health Food, Jing Brand Co. Ltd, Daye, China
| | - Liang Chen
- Hubei Key Laboratory of Quality and Safety of Traditional Chinese Medicine and Health Food, Jing Brand Co. Ltd, Daye, China
| | - Lei Zhang
- Hubei Key Laboratory of Quality and Safety of Traditional Chinese Medicine and Health Food, Jing Brand Co. Ltd, Daye, China
| | - Gang Zhang
- Hubei Key Laboratory of Quality and Safety of Traditional Chinese Medicine and Health Food, Jing Brand Co. Ltd, Daye, China
| | - Bin Lin
- Hubei Key Laboratory of Quality and Safety of Traditional Chinese Medicine and Health Food, Jing Brand Co. Ltd, Daye, China
| | - Jie Tang
- Hubei Key Laboratory of Quality and Safety of Traditional Chinese Medicine and Health Food, Jing Brand Co. Ltd, Daye, China
| | - Zongjie Zhang
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, College of Life Sciences, Hubei Normal University, Huangshi, China
| | - Shenxi Chen
- Hubei Key Laboratory of Quality and Safety of Traditional Chinese Medicine and Health Food, Jing Brand Co. Ltd, Daye, China
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10
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Tatli M, Moraïs S, Tovar-Herrera OE, Bomble YJ, Bayer EA, Medalia O, Mizrahi I. Nanoscale resolution of microbial fiber degradation in action. eLife 2022; 11:76523. [PMID: 35638899 PMCID: PMC9191890 DOI: 10.7554/elife.76523] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 05/30/2022] [Indexed: 11/18/2022] Open
Abstract
The lives of microbes unfold at the micron scale, and their molecular machineries operate at the nanoscale. Their study at these resolutions is key toward achieving a better understanding of their ecology. We focus on cellulose degradation of the canonical Clostridium thermocellum system to comprehend how microbes build and use their cellulosomal machinery at these nanometer scales. Degradation of cellulose, the most abundant organic polymer on Earth, is instrumental to the global carbon cycle. We reveal that bacterial cells form ‘cellulosome capsules’ driven by catalytic product-dependent dynamics, which can increase the rate of hydrolysis. Biosynthesis of this energetically costly machinery and cell growth are decoupled at the single-cell level, hinting at a division-of-labor strategy through phenotypic heterogeneity. This novel observation highlights intrapopulation interactions as key to understanding rates of fiber degradation.
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Affiliation(s)
- Meltem Tatli
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Sarah Moraïs
- Faculty of Natural Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Omar E Tovar-Herrera
- Faculty of Natural Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | | | - Edward A Bayer
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Ohad Medalia
- Department of Biochemistry, University of Zürich, Zurich, Switzerland
| | - Itzhak Mizrahi
- Faculty of Natural Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
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11
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Ichikawa S, Ito D, Asaoka S, Abe R, Katsuo N, Ito T, Ito D, Karita S. The expression of alternative sigma-I7 factor induces the transcription of cellulosomal genes in the cellulolytic bacterium Clostridium thermocellum. Enzyme Microb Technol 2022; 156:110002. [DOI: 10.1016/j.enzmictec.2022.110002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 01/12/2022] [Accepted: 01/31/2022] [Indexed: 01/07/2023]
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12
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Gardner JG, Schreier HJ. Unifying themes and distinct features of carbon and nitrogen assimilation by polysaccharide-degrading bacteria: a summary of four model systems. Appl Microbiol Biotechnol 2021; 105:8109-8127. [PMID: 34611726 DOI: 10.1007/s00253-021-11614-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/20/2021] [Accepted: 09/21/2021] [Indexed: 11/24/2022]
Abstract
Our current understanding of enzymatic polysaccharide degradation has come from a huge number of in vitro studies with purified enzymes. While this vast body of work has been invaluable in identifying and characterizing novel mechanisms of action and engineering desirable traits into these enzymes, a comprehensive picture of how these enzymes work as part of a native in vivo system is less clear. Recently, several model bacteria have emerged with genetic systems that allow for a more nuanced study of carbohydrate active enzymes (CAZymes) and how their activity affects bacterial carbon metabolism. With these bacterial model systems, it is now possible to not only study a single nutrient system in isolation (i.e., carbohydrate degradation and carbon metabolism), but also how multiple systems are integrated. Given that most environmental polysaccharides are carbon rich but nitrogen poor (e.g., lignocellulose), the interplay between carbon and nitrogen metabolism in polysaccharide-degrading bacteria can now be studied in a physiologically relevant manner. Therefore, in this review, we have summarized what has been experimentally determined for CAZyme regulation, production, and export in relation to nitrogen metabolism for two Gram-positive (Caldicellulosiruptor bescii and Clostridium thermocellum) and two Gram-negative (Bacteroides thetaiotaomicron and Cellvibrio japonicus) polysaccharide-degrading bacteria. By comparing and contrasting these four bacteria, we have highlighted the shared and unique features of each, with a focus on in vivo studies, in regard to carbon and nitrogen assimilation. We conclude with what we believe are two important questions that can act as guideposts for future work to better understand the integration of carbon and nitrogen metabolism in polysaccharide-degrading bacteria. KEY POINTS: • Regardless of CAZyme deployment system, the generation of a local pool of oligosaccharides is a common strategy among Gram-negative and Gram-positive polysaccharide degraders as a means to maximally recoup the energy expenditure of CAZyme production and export. • Due to the nitrogen deficiency of insoluble polysaccharide-containing substrates, Gram-negative and Gram-positive polysaccharide degraders have a diverse set of strategies for supplementation and assimilation. • Future work needs to precisely characterize the energetic expenditures of CAZyme deployment and bolster our understanding of how carbon and nitrogen metabolism are integrated in both Gram-negative and Gram-positive polysaccharide-degrading bacteria, as both of these will significantly influence a given bacterium's suitability for biotechnology applications.
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Affiliation(s)
- Jeffrey G Gardner
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD, USA.
| | - Harold J Schreier
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD, USA.,Department of Marine Biotechnology, Institute of Marine and Environmental Technology, University of Maryland, Baltimore County, Baltimore, MD, USA
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13
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Hebdon SD, Gerritsen AT, Chen YP, Marcano JG, Chou KJ. Genome-Wide Transcription Factor DNA Binding Sites and Gene Regulatory Networks in Clostridium thermocellum. Front Microbiol 2021; 12:695517. [PMID: 34566906 PMCID: PMC8457756 DOI: 10.3389/fmicb.2021.695517] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 07/27/2021] [Indexed: 12/02/2022] Open
Abstract
Clostridium thermocellum is a thermophilic bacterium recognized for its natural ability to effectively deconstruct cellulosic biomass. While there is a large body of studies on the genetic engineering of this bacterium and its physiology to-date, there is limited knowledge in the transcriptional regulation in this organism and thermophilic bacteria in general. The study herein is the first report of a large-scale application of DNA-affinity purification sequencing (DAP-seq) to transcription factors (TFs) from a bacterium. We applied DAP-seq to > 90 TFs in C. thermocellum and detected genome-wide binding sites for 11 of them. We then compiled and aligned DNA binding sequences from these TFs to deduce the primary DNA-binding sequence motifs for each TF. These binding motifs are further validated with electrophoretic mobility shift assay (EMSA) and are used to identify individual TFs’ regulatory targets in C. thermocellum. Our results led to the discovery of novel, uncharacterized TFs as well as homologues of previously studied TFs including RexA-, LexA-, and LacI-type TFs. We then used these data to reconstruct gene regulatory networks for the 11 TFs individually, which resulted in a global network encompassing the TFs with some interconnections. As gene regulation governs and constrains how bacteria behave, our findings shed light on the roles of TFs delineated by their regulons, and potentially provides a means to enable rational, advanced genetic engineering of C. thermocellum and other organisms alike toward a desired phenotype.
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Affiliation(s)
- Skyler D Hebdon
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Alida T Gerritsen
- Computational Sciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Yi-Pei Chen
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Joan G Marcano
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Katherine J Chou
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
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14
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Zhuang H, Lee PH, Wu Z, Jing H, Guan J, Tang X, Tan GYA, Leu SY. Genomic driven factors enhance biocatalyst-related cellulolysis potential in anaerobic digestion. BIORESOURCE TECHNOLOGY 2021; 333:125148. [PMID: 33878497 DOI: 10.1016/j.biortech.2021.125148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 04/01/2021] [Accepted: 04/04/2021] [Indexed: 06/12/2023]
Abstract
Anaerobic digestion (AD) is a promising technology to recover bioenergy from biodegradable biomass, including cellulosic wastes. Through a few fractionation/separation techniques, cellulose has demonstrated its potential in AD, but the performance of the process is rather substrate-specific, as cellulolysis bacteria are sensitive to the enzyme-substrate interactions. Cellulosome is a self-assembled enzyme complex with many functionalized modules in the bacteria which has been gradually studied, however the genomic fingerprints of the culture-specific cellulosome in AD are relatively unclear especially under processing conditions. To clarify the key factors affecting the cellulosome induced cellulolysis, this review summarized the most recent publications of AD regarding the fates of cellulose, sources and functional genes of cellulosome, and omics methods for functional analyses. Different processes for organic treatment including applying food grinds in sewer, biomass valorization, cellulose fractionation, microaeration, and enzymatic hydrolysis enhanced fermentation, were highlighted to support the sustainable development of AD technology.
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Affiliation(s)
- Huichuan Zhuang
- Dept. of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong; Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Po-Heng Lee
- Dept. of Civil and Environmental Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Zhuoying Wu
- Dept. of Civil and Environmental Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Houde Jing
- Dept. of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Jianyu Guan
- Dept. of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Xiaojing Tang
- Dept. of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Giin-Yu Amy Tan
- Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Shao-Yuan Leu
- Dept. of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong.
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15
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Utilization of Monosaccharides by Hungateiclostridium thermocellum ATCC 27405 through Adaptive Evolution. Microorganisms 2021; 9:microorganisms9071445. [PMID: 34361881 PMCID: PMC8303734 DOI: 10.3390/microorganisms9071445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 06/30/2021] [Accepted: 07/02/2021] [Indexed: 12/13/2022] Open
Abstract
Hungateiclostridium thermocellum ATCC 27405 is a promising bacterium for consolidated bioprocessing with a robust ability to degrade lignocellulosic biomass through a multienzyme cellulosomal complex. The bacterium uses the released cellodextrins, glucose polymers of different lengths, as its primary carbon source and energy. In contrast, the bacterium exhibits poor growth on monosaccharides such as fructose and glucose. This phenomenon raises many important questions concerning its glycolytic pathways and sugar transport systems. Until now, the detailed mechanisms of H. thermocellum adaptation to growth on hexose sugars have been relatively poorly explored. In this study, adaptive laboratory evolution was applied to train the bacterium in hexose sugars-based media, and genome resequencing was used to detect the genes that got mutated during adaptation period. RNA-seq data of the first culture growing on either fructose or glucose revealed that several glycolytic genes in the Embden–Mayerhof–Parnas pathway were expressed at lower levels in these cells than in cellobiose-grown cells. After seven consecutive transfer events on fructose and glucose (~42 generations for fructose-adapted cells and ~40 generations for glucose-adapted cells), several genes in the EMP glycolysis of the evolved strains increased the levels of mRNA expression, accompanied by a faster growth, a greater biomass yield, a higher ethanol titer than those in their parent strains. Genomic screening also revealed several mutation events in the genomes of the evolved strains, especially in those responsible for sugar transport and central carbon metabolism. Consequently, these genes could be applied as potential targets for further metabolic engineering to improve this bacterium for bio-industrial usage.
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16
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Vera AM, Galera-Prat A, Wojciechowski M, Różycki B, Laurents DV, Carrión-Vázquez M, Cieplak M, Tinnefeld P. Cohesin-dockerin code in cellulosomal dual binding modes and its allosteric regulation by proline isomerization. Structure 2021; 29:587-597.e8. [PMID: 33561387 DOI: 10.1016/j.str.2021.01.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/25/2020] [Accepted: 01/11/2021] [Indexed: 12/20/2022]
Abstract
Cellulose is the most abundant organic molecule on Earth and represents a renewable and practically everlasting feedstock for the production of biofuels and chemicals. Self-assembled owing to the high-affinity cohesin-dockerin interaction, cellulosomes are huge multi-enzyme complexes with unmatched efficiency in the degradation of recalcitrant lignocellulosic substrates. The recruitment of diverse dockerin-borne enzymes into a multicohesin protein scaffold dictates the three-dimensional layout of the complex, and interestingly two alternative binding modes have been proposed. Using single-molecule fluorescence resonance energy transfer and molecular simulations on a range of cohesin-dockerin pairs, we directly detect varying distributions between these binding modes that follow a built-in cohesin-dockerin code. Surprisingly, we uncover a prolyl isomerase-modulated allosteric control mechanism, mediated by the isomerization state of a single proline residue, which regulates the distribution and kinetics of binding modes. Overall, our data provide a novel mechanistic understanding of the structural plasticity and dynamics of cellulosomes.
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Affiliation(s)
- Andrés Manuel Vera
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13 Haus E, 81377 München, Germany.
| | - Albert Galera-Prat
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014 Oulu, Finland
| | - Michał Wojciechowski
- Institute of Physics, Polish Academy of Sciences, Al. Lotników, 32/46, 02-668 Warsaw, Poland
| | - Bartosz Różycki
- Institute of Physics, Polish Academy of Sciences, Al. Lotników, 32/46, 02-668 Warsaw, Poland
| | - Douglas V Laurents
- Instituto de Química Física "Rocasolano", CSIC, C/ Serrano 119, 28006 Madrid, Spain
| | | | - Marek Cieplak
- Institute of Physics, Polish Academy of Sciences, Al. Lotników, 32/46, 02-668 Warsaw, Poland
| | - Philip Tinnefeld
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13 Haus E, 81377 München, Germany
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17
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Yayo J, Kuil T, Olson DG, Lynd LR, Holwerda EK, van Maris AJA. Laboratory Evolution and Reverse Engineering of Clostridium thermocellum for Growth on Glucose and Fructose. Appl Environ Microbiol 2021; 87:e03017-20. [PMID: 33608285 PMCID: PMC8091016 DOI: 10.1128/aem.03017-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 02/10/2021] [Indexed: 02/04/2023] Open
Abstract
The native ability of Clostridium thermocellum to efficiently solubilize cellulose makes it an interesting platform for sustainable biofuel production through consolidated bioprocessing. Together with other improvements, industrial implementation of C. thermocellum, as well as fundamental studies into its metabolism, would benefit from improved and reproducible consumption of hexose sugars. To investigate growth of C. thermocellum on glucose or fructose, as well as the underlying molecular mechanisms, laboratory evolution was performed in carbon-limited chemostats with increasing concentrations of glucose or fructose and decreasing cellobiose concentrations. Growth on both glucose and fructose was achieved with biomass yields of 0.09 ± 0.00 and 0.18 ± 0.00 gbiomass gsubstrate-1, respectively, compared to 0.15 ± 0.01 gbiomass gsubstrate-1 for wild type on cellobiose. Single-colony isolates had no or short lag times on the monosaccharides, while wild type showed 42 ± 4 h on glucose and >80 h on fructose. With good growth on glucose, fructose, and cellobiose, the fructose isolates were chosen for genome sequence-based reverse metabolic engineering. Deletion of a putative transcriptional regulator (Clo1313_1831), which upregulated fructokinase activity, reduced lag time on fructose to 12 h with a growth rate of 0.11 ± 0.01 h-1 and resulted in immediate growth on glucose at 0.24 ± 0.01 h-1 Additional introduction of a G-to-V mutation at position 148 in cbpA resulted in immediate growth on fructose at 0.32 ± 0.03 h-1 These insights can guide engineering of strains for fundamental studies into transport and the upper glycolysis, as well as maximizing product yields in industrial settings.IMPORTANCEC. thermocellum is an important candidate for sustainable and cost-effective production of bioethanol through consolidated bioprocessing. In addition to unsurpassed cellulose deconstruction, industrial application and fundamental studies would benefit from improvement of glucose and fructose consumption. This study demonstrated that C. thermocellum can be evolved for reproducible constitutive growth on glucose or fructose. Subsequent genome sequencing, gene editing, and physiological characterization identified two underlying mutations with a role in (regulation of) transport or metabolism of the hexose sugars. In light of these findings, such mutations have likely (and unknowingly) also occurred in previous studies with C. thermocellum using hexose-based media with possible broad regulatory consequences. By targeted modification of these genes, industrial and research strains of C. thermocellum can be engineered to (i) reduce glucose accumulation, (ii) study cellodextrin transport systems in vivo, (iii) allow experiments at >120 g liter-1 soluble substrate concentration, or (iv) reduce costs for labeling studies.
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Affiliation(s)
- Johannes Yayo
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Teun Kuil
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Daniel G Olson
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Lee R Lynd
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Evert K Holwerda
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Antonius J A van Maris
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
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18
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Rico JL, Reardon KF, De Long SK. Inoculum microbiome composition impacts fatty acid product profile from cellulosic feedstock. BIORESOURCE TECHNOLOGY 2021; 323:124532. [PMID: 33422791 DOI: 10.1016/j.biortech.2020.124532] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 12/07/2020] [Accepted: 12/08/2020] [Indexed: 06/12/2023]
Abstract
Conversion of organic wastes to fatty acids rather than methane through anaerobic digestion-based technologies has considerable promise. However, the relationships between microbiome structure and fatty acids produced from cellulosic feedstocks are not well understood. This study investigated the nature of those relationships for anaerobic digester sludge, bison rumen, and cattle rumen inocula grown on cellulose. Acetic acid production was highest in anaerobic sludge reactors, while propionic acid production was highest in cattle rumen reactors. Butyric and pentanoic acid were produced at the highest rates in bison rumen before Day 5. Reactor microbiomes remained distinct, despite identical operating conditions. Novel associations linked Alistipes with butyric acid production and Eubacterium nodatum and Clostridiales bacterium with pentanoic acid production. This study provides new insights into the ability of microbiomes to convert cellulose to different fatty acid mixtures and adds impetus for the rewiring of anaerobic digestion to generate high-value products.
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Affiliation(s)
- Jorge L Rico
- Department of Civil and Environmental Engineering, Colorado State University, 1301 Campus Delivery, Fort Collins, CO 80523, USA.
| | - Kenneth F Reardon
- Department of Chemical and Biological Engineering, Colorado State University, 1301 Campus Delivery, Fort Collins, CO 80523, USA.
| | - Susan K De Long
- Department of Civil and Environmental Engineering, Colorado State University, 1301 Campus Delivery, Fort Collins, CO 80523, USA.
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19
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Chettri D, Verma AK, Verma AK. Innovations in CAZyme gene diversity and its modification for biorefinery applications. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2020; 28:e00525. [PMID: 32963975 PMCID: PMC7490808 DOI: 10.1016/j.btre.2020.e00525] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/04/2020] [Accepted: 08/30/2020] [Indexed: 02/07/2023]
Abstract
For sustainable growth, concept of biorefineries as recourse to the "fossil derived" energy source is important. Here, the Carbohydrate Active enZymes (CAZymes) play decisive role in generation of biofuels and related sugar-based products utilizing lignocellulose as a carbon source. Given their industrial significance, extensive studies on the evolution of CAZymes have been carried out. Various bacterial and fungal organisms have been scrutinized for the development of CAZymes, where advance techniques for strain enhancement such as CRISPR and analysis of specific expression systems have been deployed. Specific Omic-based techniques along with protein engineering have been adopted to unearth novel CAZymes and improve applicability of existing enzymes. In-Silico computational research and functional annotation of new CAZymes to synergy experiments are being carried out to devise cocktails of enzymes for use in biorefineries. Thus, with the establishment of these technologies, increased diversity of CAZymes with broad span of functions and applications is seen.
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20
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Transcriptomic analysis of a Clostridium thermocellum strain engineered to utilize xylose: responses to xylose versus cellobiose feeding. Sci Rep 2020; 10:14517. [PMID: 32884054 PMCID: PMC7471329 DOI: 10.1038/s41598-020-71428-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 08/10/2020] [Indexed: 12/20/2022] Open
Abstract
Clostridium (Ruminiclostridium) thermocellum is recognized for its ability to ferment cellulosic biomass directly, but it cannot naturally grow on xylose. Recently, C. thermocellum (KJC335) was engineered to utilize xylose through expressing a heterologous xylose catabolizing pathway. Here, we compared KJC335′s transcriptomic responses to xylose versus cellobiose as the primary carbon source and assessed how the bacteria adapted to utilize xylose. Our analyses revealed 417 differentially expressed genes (DEGs) with log2 fold change (FC) >|1| and 106 highly DEGs (log2 FC >|2|). Among the DEGs, two putative sugar transporters, cbpC and cbpD, were up-regulated, suggesting their contribution to xylose transport and assimilation. Moreover, the up-regulation of specific transketolase genes (tktAB) suggests the importance of this enzyme for xylose metabolism. Results also showed remarkable up-regulation of chemotaxis and motility associated genes responding to xylose feeding, as well as widely varying gene expression in those encoding cellulosomal enzymes. For the down-regulated genes, several were categorized in gene ontology terms oxidation–reduction processes, ATP binding and ATPase activity, and integral components of the membrane. This study informs potentially critical, enabling mechanisms to realize the conceptually attractive Next-Generation Consolidated BioProcessing approach where a single species is sufficient for the co-fermentation of cellulose and hemicellulose.
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21
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In Vivo Thermodynamic Analysis of Glycolysis in Clostridium thermocellum and Thermoanaerobacterium saccharolyticum Using 13C and 2H Tracers. mSystems 2020; 5:5/2/e00736-19. [PMID: 32184362 PMCID: PMC7380578 DOI: 10.1128/msystems.00736-19] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Thermodynamics constitutes a key determinant of flux and enzyme efficiency in metabolic networks. Here, we provide new insights into the divergent thermodynamics of the glycolytic pathways of C. thermocellum and T. saccharolyticum, two industrially relevant thermophilic bacteria whose metabolism still is not well understood. We report that while the glycolytic pathway in T. saccharolyticum is as thermodynamically favorable as that found in model organisms, such as E. coli or Saccharomyces cerevisiae, the glycolytic pathway of C. thermocellum operates near equilibrium. The use of a near-equilibrium glycolytic pathway, with potentially increased ATP yield, by this cellulolytic microbe may represent an evolutionary adaptation to growth on cellulose, but it has the drawback of being highly susceptible to product feedback inhibition. The results of this study will facilitate future engineering of high-performance strains capable of transforming cellulosic biomass to biofuels at high yields and titers. Clostridium thermocellum and Thermoanaerobacterium saccharolyticum are thermophilic anaerobic bacteria with complementary metabolic capabilities that utilize distinct glycolytic pathways for the conversion of cellulosic sugars to biofuels. We integrated quantitative metabolomics with 2H and 13C metabolic flux analysis to investigate the in vivo reversibility and thermodynamics of the central metabolic networks of these two microbes. We found that the glycolytic pathway in C. thermocellum operates remarkably close to thermodynamic equilibrium, with an overall drop in Gibbs free energy 5-fold lower than that of T. saccharolyticum or anaerobically grown Escherichia coli. The limited thermodynamic driving force of glycolysis in C. thermocellum could be attributed in large part to the small free energy of the phosphofructokinase reaction producing fructose bisphosphate. The ethanol fermentation pathway was also substantially more reversible in C. thermocellum than in T. saccharolyticum. These observations help explain the comparatively low ethanol titers of C. thermocellum and suggest engineering interventions that can be used to increase its ethanol productivity and glycolytic rate. In addition to thermodynamic analysis, we used our isotope tracer data to reconstruct the T. saccharolyticum central metabolic network, revealing exclusive use of the Embden-Meyerhof-Parnas (EMP) pathway for glycolysis, a bifurcated tricarboxylic acid (TCA) cycle, and a sedoheptulose bisphosphate bypass active within the pentose phosphate pathway. IMPORTANCE Thermodynamics constitutes a key determinant of flux and enzyme efficiency in metabolic networks. Here, we provide new insights into the divergent thermodynamics of the glycolytic pathways of C. thermocellum and T. saccharolyticum, two industrially relevant thermophilic bacteria whose metabolism still is not well understood. We report that while the glycolytic pathway in T. saccharolyticum is as thermodynamically favorable as that found in model organisms, such as E. coli or Saccharomyces cerevisiae, the glycolytic pathway of C. thermocellum operates near equilibrium. The use of a near-equilibrium glycolytic pathway, with potentially increased ATP yield, by this cellulolytic microbe may represent an evolutionary adaptation to growth on cellulose, but it has the drawback of being highly susceptible to product feedback inhibition. The results of this study will facilitate future engineering of high-performance strains capable of transforming cellulosic biomass to biofuels at high yields and titers.
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22
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Wei Z, Chen C, Liu YJ, Dong S, Li J, Qi K, Liu S, Ding X, Ortiz de Ora L, Muñoz-Gutiérrez I, Li Y, Yao H, Lamed R, Bayer EA, Cui Q, Feng Y. Alternative σI/anti-σI factors represent a unique form of bacterial σ/anti-σ complex. Nucleic Acids Res 2019; 47:5988-5997. [PMID: 31106374 PMCID: PMC6582324 DOI: 10.1093/nar/gkz355] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 04/21/2019] [Accepted: 04/26/2019] [Indexed: 12/18/2022] Open
Abstract
The σ70 family alternative σI factors and their cognate anti-σI factors are widespread in Clostridia and Bacilli and play a role in heat stress response, virulence, and polysaccharide sensing. Multiple σI/anti-σI factors exist in some lignocellulolytic clostridial species, specifically for regulation of components of a multienzyme complex, termed the cellulosome. The σI and anti-σI factors are unique, because the C-terminal domain of σI (SigIC) and the N-terminal inhibitory domain of anti-σI (RsgIN) lack homology to known proteins. Here, we report structure and interaction studies of a pair of σI and anti-σI factors, SigI1 and RsgI1, from the cellulosome-producing bacterium, Clostridium thermocellum. In contrast to other known anti-σ factors that have N-terminal helical structures, RsgIN has a β-barrel structure. Unlike other anti-σ factors that bind both σ2 and σ4 domains of the σ factors, RsgIN binds SigIC specifically. Structural analysis showed that SigIC contains a positively charged surface region that recognizes the promoter -35 region, and the synergistic interactions among multiple interfacial residues result in the specificity displayed by different σI/anti-σI pairs. We suggest that the σI/anti-σI factors represent a distinctive mode of σ/anti-σ complex formation, which provides the structural basis for understanding the molecular mechanism of the intricate σI/anti-σI system.
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Affiliation(s)
- Zhen Wei
- CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chao Chen
- CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Ya-Jun Liu
- CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Sheng Dong
- CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Jie Li
- CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kuan Qi
- CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shiyue Liu
- CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoke Ding
- CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Lizett Ortiz de Ora
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Iván Muñoz-Gutiérrez
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Yifei Li
- CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Hongwei Yao
- High-Field Nuclear Magnetic Resonance Center, Xiamen University, 422 South Siming Road, Xiamen 361005, China
| | - Raphael Lamed
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Edward A Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Qiu Cui
- CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Yingang Feng
- CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- To whom correspondence should be addressed. Tel: +86 532 80662706; Fax: +86 532 80662707;
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Ichikawa S, Ogawa S, Nishida A, Kobayashi Y, Kurosawa T, Karita S. Cellulosomes localise on the surface of membrane vesicles from the cellulolytic bacterium Clostridium thermocellum. FEMS Microbiol Lett 2019; 366:5526221. [DOI: 10.1093/femsle/fnz145] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 06/27/2019] [Indexed: 12/21/2022] Open
Abstract
ABSTRACTMembrane vesicles released from bacteria contribute to cell–cell communication by carrying various cargos such as proteins, nucleic acids and signaling molecules. Cellulolytic bacteria have been isolated from many environments, yet the function of membrane vesicles for cellulolytic ability has been rarely described. Here, we show that a Gram-positive cellulolytic bacterium Clostridium thermocellum released membrane vesicles, each approximately 50–300 nm in diameter, into the broth. The observations with immunoelectron microscopy also revealed that cellulosomes, which are carbohydrate-active enzyme complexes that give C. thermocellum high cellulolytic activity, localized on the surface of the membrane vesicles. The membrane vesicles collected by ultracentrifugation maintained the cellulolytic activity. Supplementation with the biosurfactant surfactin or sonication treatment disrupted the membrane vesicles in the exoproteome of C. thermocellum and significantly decreased the degradation activity of the exoproteome for microcrystalline cellulose. However, these did not affect the degradation activity for soluble carboxymethyl cellulose. These results suggest a novel function of membrane vesicles: C. thermocellum releases cellulolytic enzymes on the surface of membrane vesicles to enhance the cellulolytic activity of C. thermocellum for crystalline cellulose.
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Affiliation(s)
- Shunsuke Ichikawa
- Graduate School of Education, Mie University, 1577 Kurimamachiya-cho Tsu, Mie 514-8507, Japan
| | - Satoru Ogawa
- Faculty of Medicine, Mie University, 1577 Kurimamachiya-cho Tsu, Mie 514-8507, Japan
| | - Ayami Nishida
- Graduate School of Education, Mie University, 1577 Kurimamachiya-cho Tsu, Mie 514-8507, Japan
| | - Yuzuki Kobayashi
- Faculty of Education, Mie University, 1577 Kurimamachiya-cho Tsu, Mie 514-8507, Japan
| | - Toshihito Kurosawa
- Advanced Science Research Promotion Center, Mie University, 1577 Kurimamachiya-cho Tsu, Mie 514-8507, Japan
| | - Shuichi Karita
- Graduate School of Bioresources, Mie University, 1577 Kurimamachiya-cho Tsu, Mie 514-8507, Japan
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24
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Sahoo K, Sahoo RK, Gaur M, Subudhi E. Cellulolytic thermophilic microorganisms in white biotechnology: a review. Folia Microbiol (Praha) 2019; 65:25-43. [DOI: 10.1007/s12223-019-00710-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 04/15/2019] [Indexed: 10/26/2022]
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Zhivin-Nissan O, Dassa B, Morag E, Kupervaser M, Levin Y, Bayer EA. Unraveling essential cellulosomal components of the ( Pseudo) Bacteroides cellulosolvens reveals an extensive reservoir of novel catalytic enzymes. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:115. [PMID: 31086567 PMCID: PMC6507058 DOI: 10.1186/s13068-019-1447-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 04/20/2019] [Indexed: 05/23/2023]
Abstract
BACKGROUND (Pseudo)Bacteroides cellulosolvens is a cellulolytic bacterium that produces the most extensive and intricate cellulosomal system known in nature. Recently, the elaborate architecture of the B. cellulosolvens cellulosomal system was revealed from analysis of its genome sequence, and the first evidence regarding the interactions between its structural and enzymatic components were detected in vitro. Yet, the understanding of the cellulolytic potential of the bacterium in carbohydrate deconstruction is inextricably linked to its high-molecular-weight protein complexes, which are secreted from the bacterium. RESULTS The current proteome-wide work reveals patterns of protein expression of the various cellulosomal components, and explores the signature of differential expression upon growth of the bacterium on two major carbon sources-cellobiose and microcrystalline cellulose. Mass spectrometry analysis of the bacterial secretome revealed the expression of 24 scaffoldin structural units and 166 dockerin-bearing components (mainly enzymes), in addition to free enzymatic subunits. The dockerin-bearing components comprise cell-free and cell-bound cellulosomes for more efficient carbohydrate degradation. Various glycoside hydrolase (GH) family members were represented among 102 carbohydrate-degrading enzymes, including the omnipresent, most abundant GH48 exoglucanase. Specific cellulosomal components were found in different molecular-weight fractions associated with cell growth on different carbon sources. Overall, microcrystalline cellulose-derived cellulosomes showed markedly higher expression levels of the structural and enzymatic components, and exhibited the highest degradation activity on five different cellulosic and/or hemicellulosic carbohydrates. The cellulosomal activity of B. cellulosolvens showed high degradation rates that are very promising in biotechnological terms and were compatible with the activity levels exhibited by Clostridium thermocellum purified cellulosomes. CONCLUSIONS The current research demonstrates the involvement of key cellulosomal factors that participate in the mechanism of carbohydrate degradation by B. cellulosolvens. The powerful ability of the bacterium to exhibit different degradation strategies on various carbon sources was revealed. The novel reservoir of cellulolytic components of the cellulosomal degradation machineries may serve as a pool for designing new cellulolytic cocktails for biotechnological purposes.
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Affiliation(s)
- Olga Zhivin-Nissan
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Bareket Dassa
- Bioinformatics Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Ely Morag
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Meital Kupervaser
- Proteomics Unit, Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Yishai Levin
- Proteomics Unit, Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Edward A. Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
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26
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Chen C, Yang H, Xuan J, Cui Q, Feng Y. Resonance assignments of a cellulosomal double-dockerin from Clostridium thermocellum. BIOMOLECULAR NMR ASSIGNMENTS 2019; 13:97-101. [PMID: 30377946 DOI: 10.1007/s12104-018-9859-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 10/24/2018] [Indexed: 06/08/2023]
Abstract
Cellulosomes are highly efficient multienzyme complexes for lignocellulose degradation secreted by some lignocellulolytic bacteria. Cellulosomes are assembled through protein modules named cohesin and dockerin, and multiple cohesin modules in the scaffold protein generally determine the complexity of the cellulosomes. Some cellulosomal proteins contain multiple dockerin modules, which may generate more complex cellulosomal architectures. Genome mining revealed that cellulosomal proteins containing double dockerin modules and a protease module exist in many cellulosome-producing bacteria, and these proteins together with cellulosomal protease inhibitors were proposed to have regulatory roles. However, the structures and functions of these multiple-dockerin proteins in cellulosome have not been reported before. In this paper, we present the NMR chemical shift assignments of the double-dockerin of a cellulosomal protease from Clostridium thermocellum DSM1313. The secondary structures predicted from the chemical shifts agree with the structural arrangement of the tandem dockerin modules. The chemical shift assignments here provide the basis for the structural and functional studies of multiple-dockerin proteins in future.
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Affiliation(s)
- Chao Chen
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Hongwu Yang
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Jinsong Xuan
- Department of Biological Science and Engineering, School of Chemical and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Beijing, 100083, China
| | - Qiu Cui
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Yingang Feng
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.
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27
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Liu S, Liu YJ, Feng Y, Li B, Cui Q. Construction of consolidated bio-saccharification biocatalyst and process optimization for highly efficient lignocellulose solubilization. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:35. [PMID: 30820245 PMCID: PMC6378752 DOI: 10.1186/s13068-019-1374-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 02/07/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND The industrial conversion of biomass to high-value biofuels and biochemical is mainly restricted by lignocellulose solubilization. Consolidated bio-saccharification (CBS) is considered a promising process for lignocellulose solubilization depending on whole-cell biocatalysts that simultaneously perform effective cellulase production and hydrolysis. However, it usually takes a long time to reach a high saccharification level using the current CBS biocatalyst and process. RESULTS To promote the saccharification efficiency and reduce the cost, a Clostridium thermocellum recombinant strain ∆pyrF::KBm was constructed as a new CBS biocatalyst in this study. The key CBS factors, including the medium, inoculum size and cultivation, and substrate load, were investigated and optimized. The saccharification process was also stimulated by adding free hemicellulases, suggesting the need to further enhance hemicellulase activity of the whole-cell catalyst. Under the optimal conditions, the CBS process was shortened by 50% with pretreated wheat straw as the substrate. The sugar yield reached 0.795 g/g and the saccharification level was 89.3%. CONCLUSIONS This work provided a new biocatalyst and an optimized process of CBS and confirmed that CBS is a feasible strategy for cost-efficient solubilization of lignocellulose, which will greatly promote the industrial utilization of lignocellulosic biomass.
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Affiliation(s)
- Shiyue Liu
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Dalian National Laboratory for Clean Energy, Chinese Academy of Sciences, Dalian, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Ya-Jun Liu
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Dalian National Laboratory for Clean Energy, Chinese Academy of Sciences, Dalian, China
| | - Yingang Feng
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Dalian National Laboratory for Clean Energy, Chinese Academy of Sciences, Dalian, China
| | - Bin Li
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Dalian National Laboratory for Clean Energy, Chinese Academy of Sciences, Dalian, China
| | - Qiu Cui
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Dalian National Laboratory for Clean Energy, Chinese Academy of Sciences, Dalian, China
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28
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Characterization of the Clostridium thermocellum AdhE, NfnAB, ferredoxin and Pfor proteins for their ability to support high titer ethanol production in Thermoanaerobacterium saccharolyticum. Metab Eng 2018; 51:32-42. [PMID: 30218716 DOI: 10.1016/j.ymben.2018.09.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 08/21/2018] [Accepted: 09/11/2018] [Indexed: 12/17/2022]
Abstract
The thermophilic anaerobes Thermoanaerobacterium saccharolyticum and Clostridium thermocellum are good candidates for lignocellulosic ethanol production. T. saccharolyticum has been successfully engineered to produce ethanol at high titer (70 g/L). The maximum ethanol titer of engineered strains of C. thermocellum is only 25 g/L. We hypothesize that one or more of the enzymes in the ethanol production pathway in C. thermocellum is not adequate for ethanol production at high titer. In this study, we focused on the enzymes responsible for the part of the ethanol production pathway from pyruvate to ethanol. In T. saccharolyticum, we replaced all of the genes encoding proteins in this pathway with their homologs from C. thermocellum and examined what combination of gene replacements restricted ethanol titer. We found that a pathway consisting of Ct_nfnAB, Ct_fd, Ct_adhE and Ts_pforA was sufficient to support ethanol titer greater than 50 g/L, however replacement of Ts_pforA by Ct_pfor1 dramatically decreased the maximum ethanol titer to 14 g/L. We then demonstrated that the reason for reduced ethanol production is that the Ct_pfor1 is inhibited by accumulation of ethanol and NADH, while Ts_pforA is not.
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29
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Hon S, Holwerda EK, Worthen RS, Maloney MI, Tian L, Cui J, Lin PP, Lynd LR, Olson DG. Expressing the Thermoanaerobacterium saccharolyticum pforA in engineered Clostridium thermocellum improves ethanol production. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:242. [PMID: 30202437 PMCID: PMC6125887 DOI: 10.1186/s13068-018-1245-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 08/27/2018] [Indexed: 05/12/2023]
Abstract
BACKGROUND Clostridium thermocellum has been the subject of multiple metabolic engineering strategies to improve its ability to ferment cellulose to ethanol, with varying degrees of success. For ethanol production in C. thermocellum, the conversion of pyruvate to acetyl-CoA is catalyzed primarily by the pyruvate ferredoxin oxidoreductase (PFOR) pathway. Thermoanaerobacterium saccharolyticum, which was previously engineered to produce ethanol of high yield (> 80%) and titer (70 g/L), also uses a pyruvate ferredoxin oxidoreductase, pforA, for ethanol production. RESULTS Here, we introduced the T. saccharolyticum pforA and ferredoxin into C. thermocellum. The introduction of pforA resulted in significant improvements to ethanol yield and titer in C. thermocellum grown on 50 g/L of cellobiose, but only when four other T. saccharolyticum genes (adhA, nfnA, nfnB, and adhEG544D ) were also present. T. saccharolyticum ferredoxin did not have any observable impact on ethanol production. The improvement to ethanol production was sustained even when all annotated native C. thermocellum pfor genes were deleted. On high cellulose concentrations, the maximum ethanol titer achieved by this engineered C. thermocellum strain from 100 g/L Avicel was 25 g/L, compared to 22 g/L for the reference strain, LL1319 (adhA(Tsc)-nfnAB(Tsc)-adhEG544D (Tsc)) under similar conditions. In addition, we also observed that deletion of the C. thermocellum pfor4 results in a significant decrease in isobutanol production. CONCLUSIONS Here, we demonstrate that the pforA gene can improve ethanol production in C. thermocellum as part of the T. saccharolyticum pyruvate-to-ethanol pathway. In our previous strain, high-yield (~ 75% of theoretical) ethanol production could be achieved with at most 20 g/L substrate. In this strain, high-yield ethanol production can be achieved up to 50 g/L substrate. Furthermore, the introduction of pforA increased the maximum titer by 14%.
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Affiliation(s)
- Shuen Hon
- Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755 USA
- Bioenergy Science Center, Oak Ridge National Laboratories, Oak Ridge, TN 37830 USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratories, Oak Ridge, TN 37830 USA
| | - Evert K. Holwerda
- Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755 USA
- Bioenergy Science Center, Oak Ridge National Laboratories, Oak Ridge, TN 37830 USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratories, Oak Ridge, TN 37830 USA
| | - Robert S. Worthen
- Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755 USA
- Bioenergy Science Center, Oak Ridge National Laboratories, Oak Ridge, TN 37830 USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratories, Oak Ridge, TN 37830 USA
| | - Marybeth I. Maloney
- Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755 USA
- Bioenergy Science Center, Oak Ridge National Laboratories, Oak Ridge, TN 37830 USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratories, Oak Ridge, TN 37830 USA
| | - Liang Tian
- Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755 USA
- Bioenergy Science Center, Oak Ridge National Laboratories, Oak Ridge, TN 37830 USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratories, Oak Ridge, TN 37830 USA
| | - Jingxuan Cui
- Bioenergy Science Center, Oak Ridge National Laboratories, Oak Ridge, TN 37830 USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratories, Oak Ridge, TN 37830 USA
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755 USA
| | - Paul P. Lin
- Bioenergy Science Center, Oak Ridge National Laboratories, Oak Ridge, TN 37830 USA
- University of California, Los Angeles, Los Angeles, CA 90095 USA
| | - Lee R. Lynd
- Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755 USA
- Bioenergy Science Center, Oak Ridge National Laboratories, Oak Ridge, TN 37830 USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratories, Oak Ridge, TN 37830 USA
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755 USA
| | - Daniel G. Olson
- Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755 USA
- Bioenergy Science Center, Oak Ridge National Laboratories, Oak Ridge, TN 37830 USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratories, Oak Ridge, TN 37830 USA
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30
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Li R, Feng Y, Liu S, Qi K, Cui Q, Liu YJ. Inducing effects of cellulosic hydrolysate components of lignocellulose on cellulosome synthesis in Clostridium thermocellum. Microb Biotechnol 2018; 11:905-916. [PMID: 29943510 PMCID: PMC6116742 DOI: 10.1111/1751-7915.13293] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 05/25/2018] [Accepted: 06/04/2018] [Indexed: 02/06/2023] Open
Abstract
Cellulosome is a highly efficient supramolecular machine for lignocellulose degradation, and its substrate‐coupled regulation requires soluble transmembrane signals. However, the inducers for cellulosome synthesis and the inducing effect have not been clarified quantitatively. Values of cellulosome production capacity (CPC) and estimated specific activity (eSA) were calculated based on the primary scaffoldin ScaA to define the stimulating effects on the cellulosome synthesis in terms of quantity and quality respectively. The estimated cellulosome production of Clostridium thermocellum on glucose was at a low housekeeping level. Both Avicel and cellobiose increased CPCs of the cells instead of the eSAs of the cellulosome. The CPC of Avicel‐grown cells was over 20‐fold of that of glucose‐grown cells, while both Avicel‐ and glucose‐derived cellulosomes showed similar eSA. The CPC of cellobiose‐grown cells was also over three times higher than glucose‐grown cells, but the eSA of cellobiose‐derived cellulosome was 16% lower than that of the glucose‐derived cellulosome. Our results indicated that cello‐oligosaccharides played the key roles in inducing the synthesis of the cellulosome, but non‐cellulosic polysaccharides showed no inducing effects.
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Affiliation(s)
- Renmin Li
- Shandong Provincial Key Laboratory of Energy Genetics, CAS Key Laboratory of Biofuels, Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.,Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yingang Feng
- Shandong Provincial Key Laboratory of Energy Genetics, CAS Key Laboratory of Biofuels, Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Shiyue Liu
- Shandong Provincial Key Laboratory of Energy Genetics, CAS Key Laboratory of Biofuels, Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.,Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Kuan Qi
- Shandong Provincial Key Laboratory of Energy Genetics, CAS Key Laboratory of Biofuels, Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.,Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Qiu Cui
- Shandong Provincial Key Laboratory of Energy Genetics, CAS Key Laboratory of Biofuels, Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Ya-Jun Liu
- Shandong Provincial Key Laboratory of Energy Genetics, CAS Key Laboratory of Biofuels, Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
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Blake AD, Beri NR, Guttman HS, Cheng R, Gardner JG. The complex physiology of
Cellvibrio japonicus
xylan degradation relies on a single cytoplasmic β‐xylosidase for xylo‐oligosaccharide utilization. Mol Microbiol 2018; 107:610-622. [DOI: 10.1111/mmi.13903] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 12/15/2017] [Accepted: 12/18/2017] [Indexed: 12/30/2022]
Affiliation(s)
- Andrew D. Blake
- Department of Biological SciencesUniversity of Maryland ‐ Baltimore CountyBaltimore Maryland USA
| | - Nina R. Beri
- Department of Biological SciencesUniversity of Maryland ‐ Baltimore CountyBaltimore Maryland USA
| | - Hadassa S. Guttman
- Department of Biological SciencesUniversity of Maryland ‐ Baltimore CountyBaltimore Maryland USA
| | - Raymond Cheng
- Department of Biological SciencesUniversity of Maryland ‐ Baltimore CountyBaltimore Maryland USA
| | - Jeffrey G. Gardner
- Department of Biological SciencesUniversity of Maryland ‐ Baltimore CountyBaltimore Maryland USA
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Attia MA, Nelson CE, Offen WA, Jain N, Davies GJ, Gardner JG, Brumer H. In vitro and in vivo characterization of three Cellvibrio japonicus glycoside hydrolase family 5 members reveals potent xyloglucan backbone-cleaving functions. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:45. [PMID: 29467823 PMCID: PMC5816542 DOI: 10.1186/s13068-018-1039-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 02/01/2018] [Indexed: 05/15/2023]
Abstract
BACKGROUND Xyloglucan (XyG) is a ubiquitous and fundamental polysaccharide of plant cell walls. Due to its structural complexity, XyG requires a combination of backbone-cleaving and sidechain-debranching enzymes for complete deconstruction into its component monosaccharides. The soil saprophyte Cellvibrio japonicus has emerged as a genetically tractable model system to study biomass saccharification, in part due to its innate capacity to utilize a wide range of plant polysaccharides for growth. Whereas the downstream debranching enzymes of the xyloglucan utilization system of C. japonicus have been functionally characterized, the requisite backbone-cleaving endo-xyloglucanases were unresolved. RESULTS Combined bioinformatic and transcriptomic analyses implicated three glycoside hydrolase family 5 subfamily 4 (GH5_4) members, with distinct modular organization, as potential keystone endo-xyloglucanases in C. japonicus. Detailed biochemical and enzymatic characterization of the GH5_4 modules of all three recombinant proteins confirmed particularly high specificities for the XyG polysaccharide versus a panel of other cell wall glycans, including mixed-linkage beta-glucan and cellulose. Moreover, product analysis demonstrated that all three enzymes generated XyG oligosaccharides required for subsequent saccharification by known exo-glycosidases. Crystallographic analysis of GH5D, which was the only GH5_4 member specifically and highly upregulated during growth on XyG, in free, product-complex, and active-site affinity-labelled forms revealed the molecular basis for the exquisite XyG specificity among these GH5_4 enzymes. Strikingly, exhaustive reverse-genetic analysis of all three GH5_4 members and a previously biochemically characterized GH74 member failed to reveal a growth defect, thereby indicating functional compensation in vivo, both among members of this cohort and by other, yet unidentified, xyloglucanases in C. japonicus. Our systems-based analysis indicates distinct substrate-sensing (GH74, GH5E, GH5F) and attack-mounting (GH5D) functions for the endo-xyloglucanases characterized here. CONCLUSIONS Through a multi-faceted, molecular systems-based approach, this study provides a new insight into the saccharification pathway of xyloglucan utilization system of C. japonicus. The detailed structural-functional characterization of three distinct GH5_4 endo-xyloglucanases will inform future bioinformatic predictions across species, and provides new CAZymes with defined specificity that may be harnessed in industrial and other biotechnological applications.
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Affiliation(s)
- Mohamed A. Attia
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T 1Z4 Canada
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1 Canada
| | - Cassandra E. Nelson
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD 21250 USA
| | - Wendy A. Offen
- Department of Chemistry, University of York, Heslington, York, YO10 5DD UK
| | - Namrata Jain
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T 1Z4 Canada
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1 Canada
| | - Gideon J. Davies
- Department of Chemistry, University of York, Heslington, York, YO10 5DD UK
| | - Jeffrey G. Gardner
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD 21250 USA
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T 1Z4 Canada
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1 Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3 Canada
- Department of Botany, University of British Columbia, 6270 University Blvd., Vancouver, BC V6T 1Z4 Canada
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33
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Yoav S, Barak Y, Shamshoum M, Borovok I, Lamed R, Dassa B, Hadar Y, Morag E, Bayer EA. How does cellulosome composition influence deconstruction of lignocellulosic substrates in Clostridium ( Ruminiclostridium) thermocellum DSM 1313? BIOTECHNOLOGY FOR BIOFUELS 2017; 10:222. [PMID: 28932263 PMCID: PMC5604425 DOI: 10.1186/s13068-017-0909-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 09/07/2017] [Indexed: 05/23/2023]
Abstract
BACKGROUND Bioethanol production processes involve enzymatic hydrolysis of pretreated lignocellulosic biomass into fermentable sugars. Due to the relatively high cost of enzyme production, the development of potent and cost-effective cellulolytic cocktails is critical for increasing the cost-effectiveness of bioethanol production. In this context, the multi-protein cellulolytic complex of Clostridium (Ruminiclostridium) thermocellum, the cellulosome, was studied here. C. thermocellum is known to assemble cellulosomes of various subunit (enzyme) compositions, in response to the available carbon source. In the current study, different carbon sources were used, and their influence on both cellulosomal composition and the resultant activity was investigated. RESULTS Glucose, cellobiose, microcrystalline cellulose, alkaline-pretreated switchgrass, alkaline-pretreated corn stover, and dilute acid-pretreated corn stover were used as sole carbon sources in the growth media of C. thermocellum strain DSM 1313. The purified cellulosomes were compared for their activity on selected cellulosic substrates. Interestingly, cellulosomes derived from cells grown on lignocellulosic biomass showed no advantage in hydrolyzing the original carbon source used for their production. Instead, microcrystalline cellulose- and glucose-derived cellulosomes were equal or superior in their capacity to deconstruct lignocellulosic biomass. Mass spectrometry analysis revealed differential composition of catalytic and structural subunits (scaffoldins) in the different cellulosome samples. The most abundant catalytic subunits in all cellulosome types include Cel48S, Cel9K, Cel9Q, Cel9R, and Cel5G. Microcrystalline cellulose- and glucose-derived cellulosome samples showed higher endoglucanase-to-exoglucanase ratios and higher catalytic subunit-per-scaffoldin ratios compared to lignocellulose-derived cellulosome types. CONCLUSION The results reported here highlight the finding that cellulosomes derived from cells grown on glucose and microcrystalline cellulose are more efficient in their action on cellulosic substrates than other cellulosome preparations. These results should be considered in the future development of C. thermocellum-based cellulolytic cocktails, designer cellulosomes, or engineering of improved strains for deconstruction of lignocellulosic biomass.
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Affiliation(s)
- Shahar Yoav
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Advanced School for Environmental Studies, The Hebrew University of Jerusalem, 76100 Rehovot, Israel
- Designer Energy Ltd, 2 Bergman Street, Rehovot, Israel
| | - Yoav Barak
- Bio-Nano Unit, Chemical Research Support, The Weizmann Institute of Science, 761000 Rehovot, Israel
| | - Melina Shamshoum
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Ilya Borovok
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Raphael Lamed
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Bareket Dassa
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Yitzhak Hadar
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Advanced School for Environmental Studies, The Hebrew University of Jerusalem, 76100 Rehovot, Israel
| | - Ely Morag
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Edward A. Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 76100 Rehovot, Israel
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Choi J, Klingeman DM, Brown SD, Cox CD. The LacI family protein GlyR3 co-regulates the celC operon and manB in Clostridium thermocellum. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:163. [PMID: 28652864 PMCID: PMC5483248 DOI: 10.1186/s13068-017-0849-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 06/16/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Clostridium thermocellum utilizes a wide variety of free and cellulosomal cellulases and accessory enzymes to hydrolyze polysaccharides present in complex substrates. To date only a few studies have unveiled the details by which the expression of these cellulases are regulated. Recent studies have described the auto regulation of the celC operon and determined that the celC-glyR3-licA gene cluster and nearby manB-celT gene cluster are co-transcribed as polycistronic mRNA. RESULTS In this paper, we demonstrate that the GlyR3 protein mediates the regulation of manB. We first identify putative GlyR3 binding sites within or just upstream of the coding regions of manB and celT. Using an electrophoretic mobility shift assay (EMSA), we determined that a higher concentration of GlyR3 is required to effectively bind to the putative manB site in comparison to the celC site. Neither the putative celT site nor random DNA significantly binds GlyR3. While laminaribiose interfered with GlyR3 binding to the celC binding site, binding to the manB site was unaffected. In the presence of laminaribiose, in vivo transcription of the celC-glyR3-licA gene cluster increases, while manB expression is repressed, compared to in the absence of laminaribiose, consistent with the results from the EMSA. An in vitro transcription assay demonstrated that GlyR3 and laminaribiose interactions were responsible for the observed patters of in vivo transcription. CONCLUSIONS Together these results reveal a mechanism by which manB is expressed at low concentrations of GlyR3 but repressed at high concentrations. In this way, C. thermocellum is able to co-regulate both the celC and manB gene clusters in response to the availability of β-1,3-polysaccharides in its environment.
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Affiliation(s)
- Jinlyung Choi
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996 USA
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996 USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Dawn M. Klingeman
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Steven D. Brown
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Chris D. Cox
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996 USA
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996 USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Department Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996 USA
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35
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Growth and expression of relevant metabolic genes of Clostridium thermocellum cultured on lignocellulosic residues. ACTA ACUST UNITED AC 2017; 44:825-834. [DOI: 10.1007/s10295-017-1915-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 01/29/2017] [Indexed: 12/31/2022]
Abstract
Abstract
The plant cell wall is a source of fermentable sugars in second-generation bioethanol production. However, cellulosic biomass hydrolysis remains an obstacle to bioethanol production in an efficient and low-cost process. Clostridium thermocellum has been studied as a model organism able to produce enzymatic blends that efficiently degrade lignocellulosic biomass, and also as a fermentative microorganism in a consolidated process for the conversion of lignocellulose to bioethanol. In this study, a C. thermocellum strain (designated B8) isolated from goat rumen was characterized for its ability to grow on sugarcane straw and cotton waste, and to produce cellulosomes. We also evaluated C. thermocellum gene expression control in the presence of complex lignocellulosic biomasses. This isolate is capable of growing in the presence of microcrystalline cellulose, sugarcane straw and cotton waste as carbon sources, producing free enzymes and residual substrate-bound proteins (RSBP). The highest growth rate and cellulase/xylanase production were detected at pH 7.0 and 60 °C, after 48 h. Moreover, this strain showed different expression levels of transcripts encoding cellulosomal proteins and proteins with a role in fermentation and catabolic repression.
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36
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Lü F, Chai L, Shao L, He P. Precise pretreatment of lignocellulose: relating substrate modification with subsequent hydrolysis and fermentation to products and by-products. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:88. [PMID: 28400859 PMCID: PMC5387280 DOI: 10.1186/s13068-017-0775-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 04/05/2017] [Indexed: 05/25/2023]
Abstract
BACKGROUND Pretreatment is a crucial step for valorization of lignocellulosic biomass into valuable products such as H2, ethanol, acids, and methane. As pretreatment can change several decisive factors concurrently, it is difficult to predict its effectiveness. Furthermore, the effectiveness of pretreatments is usually assessed by enzymatic digestibility or merely according to the yield of the target fermentation products. The present study proposed the concept of "precise pretreatment," distinguished the major decisive factors of lignocellulosic materials by precise pretreatment, and evaluated the complete profile of all fermentation products and by-products. In brief, hemicellulose and lignin were selectively removed from dewaxed rice straw, and the cellulose was further modified to alter the crystalline allomorphs. The subsequent fermentation performance of the selectively pretreated lignocellulose was assessed using the cellulolytic, ethanologenic, and hydrogenetic Clostridium thermocellum through a holistic characterization of the liquid, solid, and gaseous products and residues. RESULTS The transformation of crystalline cellulose forms from I to II and from Iα to Iβ improved the production of H2 and ethanol by 65 and 29%, respectively. At the same time, the hydrolysis efficiency was merely improved by 10%, revealing that the crystalline forms not only influenced the accessibility of cellulose but also affected the metabolic preferences and flux of the system. The fermentation efficiency was independent of the specific surface area and degree of polymerization. Furthermore, the pretreatments resulted in 43-45% of the carbon in the liquid hydrolysates unexplainable by forming ethanol and acetate products. A tandem pretreatment with peracetic acid and alkali improved ethanol production by 45.5%, but also increased the production of non-ethanolic low-value by-products by 136%, resulting in a huge burden on wastewater treatment requirements. CONCLUSION Cellulose allomorphs significantly affected fermentation metabolic pathway, except for hydrolysis efficiency. Furthermore, with the increasing effectiveness of the pretreatment for ethanol production, more non-ethanolic low-value by-products or contaminants were produced, intensifying environmental burden. Therefore, the effectiveness of the pretreatment should not only be determined on the basis of energy auditing and inhibitors generated, but should also be assessed in terms of the environmental benefits of the whole integrated system from a holistic view.
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Affiliation(s)
- Fan Lü
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai, 200092 China
| | - Lina Chai
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai, 200092 China
| | - Liming Shao
- Institute of Waste Treatment and Reclamation, Tongji University, Shanghai, 200092 China
| | - Pinjing He
- Institute of Waste Treatment and Reclamation, Tongji University, Shanghai, 200092 China
- Centre for the Technology Research and Training on Household Waste in Small Towns & Rural Area, Ministry of Housing and Urban–Rural Development (MOHURD) of China, Shanghai, 200092 China
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37
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Rydzak T, Garcia D, Stevenson DM, Sladek M, Klingeman DM, Holwerda EK, Amador-Noguez D, Brown SD, Guss AM. Deletion of Type I glutamine synthetase deregulates nitrogen metabolism and increases ethanol production in Clostridium thermocellum. Metab Eng 2017; 41:182-191. [PMID: 28400329 DOI: 10.1016/j.ymben.2017.04.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 03/27/2017] [Accepted: 04/07/2017] [Indexed: 12/25/2022]
Abstract
Clostridium thermocellum rapidly deconstructs cellulose and ferments resulting hydrolysis products into ethanol and other products, and is thus a promising platform organism for the development of cellulosic biofuel production via consolidated bioprocessing. While recent metabolic engineering strategies have targeted eliminating canonical fermentation products (acetate, lactate, formate, and H2), C. thermocellum also secretes amino acids, which has limited ethanol yields in engineered strains to approximately 70% of the theoretical maximum. To investigate approaches to decrease amino acid secretion, we attempted to reduce ammonium assimilation by deleting the Type I glutamine synthetase (glnA) in an essentially wild type strain of C. thermocellum. Deletion of glnA reduced levels of secreted valine and total amino acids by 53% and 44% respectively, and increased ethanol yields by 53%. RNA-seq analysis revealed that genes encoding the RNF-complex were more highly expressed in ΔglnA and may have a role in improving NADH-availability for ethanol production. While a significant up-regulation of genes involved in nitrogen assimilation and urea uptake suggested that deletion of glnA induces a nitrogen starvation response, metabolomic analysis showed an increase in intracellular glutamine levels indicative of nitrogen-rich conditions. We propose that deletion of glnA causes deregulation of nitrogen metabolism, leading to overexpression of nitrogen metabolism genes and, in turn, elevated glutamine levels. Here we demonstrate that perturbation of nitrogen assimilation is a promising strategy to redirect flux from the production of nitrogenous compounds toward biofuels in C. thermocellum.
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Affiliation(s)
- Thomas Rydzak
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - David Garcia
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - David M Stevenson
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
| | - Margaret Sladek
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Dawn M Klingeman
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Evert K Holwerda
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States; Thayer School of Engineering at Dartmouth College, Hanover, NH, United States
| | - Daniel Amador-Noguez
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
| | - Steven D Brown
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Adam M Guss
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States.
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38
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Dumitrache A, Klingeman DM, Natzke J, Rodriguez M, Giannone RJ, Hettich RL, Davison BH, Brown SD. Specialized activities and expression differences for Clostridium thermocellum biofilm and planktonic cells. Sci Rep 2017; 7:43583. [PMID: 28240279 PMCID: PMC5327387 DOI: 10.1038/srep43583] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 01/25/2017] [Indexed: 01/01/2023] Open
Abstract
Clostridium (Ruminiclostridium) thermocellum is a model organism for its ability to deconstruct plant biomass and convert the cellulose into ethanol. The bacterium forms biofilms adherent to lignocellulosic feedstocks in a continuous cell-monolayer in order to efficiently break down and uptake cellulose hydrolysates. We developed a novel bioreactor design to generate separate sessile and planktonic cell populations for omics studies. Sessile cells had significantly greater expression of genes involved in catabolism of carbohydrates by glycolysis and pyruvate fermentation, ATP generation by proton gradient, the anabolism of proteins and lipids and cellular functions critical for cell division consistent with substrate replete conditions. Planktonic cells had notably higher gene expression for flagellar motility and chemotaxis, cellulosomal cellulases and anchoring scaffoldins, and a range of stress induced homeostasis mechanisms such as oxidative stress protection by antioxidants and flavoprotein co-factors, methionine repair, Fe-S cluster assembly and repair in redox proteins, cell growth control through tRNA thiolation, recovery of damaged DNA by nucleotide excision repair and removal of terminal proteins by proteases. This study demonstrates that microbial attachment to cellulose substrate produces widespread gene expression changes for critical functions of this organism and provides physiological insights for two cells populations relevant for engineering of industrially-ready phenotypes.
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Affiliation(s)
- Alexandru Dumitrache
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A
| | - Dawn M Klingeman
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A
| | - Jace Natzke
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A
| | - Miguel Rodriguez
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A
| | - Richard J Giannone
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A.,Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A
| | - Robert L Hettich
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A.,Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A
| | - Brian H Davison
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A
| | - Steven D Brown
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A
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39
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Verbeke TJ, Giannone RJ, Klingeman DM, Engle NL, Rydzak T, Guss AM, Tschaplinski TJ, Brown SD, Hettich RL, Elkins JG. Pentose sugars inhibit metabolism and increase expression of an AgrD-type cyclic pentapeptide in Clostridium thermocellum. Sci Rep 2017; 7:43355. [PMID: 28230109 PMCID: PMC5322536 DOI: 10.1038/srep43355] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 01/18/2017] [Indexed: 12/22/2022] Open
Abstract
Clostridium thermocellum could potentially be used as a microbial biocatalyst to produce renewable fuels directly from lignocellulosic biomass due to its ability to rapidly solubilize plant cell walls. While the organism readily ferments sugars derived from cellulose, pentose sugars from xylan are not metabolized. Here, we show that non-fermentable pentoses inhibit growth and end-product formation during fermentation of cellulose-derived sugars. Metabolomic experiments confirmed that xylose is transported intracellularly and reduced to the dead-end metabolite xylitol. Comparative RNA-seq analysis of xylose-inhibited cultures revealed several up-regulated genes potentially involved in pentose transport and metabolism, which were targeted for disruption. Deletion of the ATP-dependent transporter, CbpD partially alleviated xylose inhibition. A putative xylitol dehydrogenase, encoded by Clo1313_0076, was also deleted resulting in decreased total xylitol production and yield by 41% and 46%, respectively. Finally, xylose-induced inhibition corresponds with the up-regulation and biogenesis of a cyclical AgrD-type, pentapeptide. Medium supplementation with the mature cyclical pentapeptide also inhibits bacterial growth. Together, these findings provide new foundational insights needed for engineering improved pentose utilizing strains of C. thermocellum and reveal the first functional Agr-type cyclic peptide to be produced by a thermophilic member of the Firmicutes.
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Affiliation(s)
- Tobin J Verbeke
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Richard J Giannone
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Dawn M Klingeman
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Nancy L Engle
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Thomas Rydzak
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Adam M Guss
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Timothy J Tschaplinski
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Steven D Brown
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Robert L Hettich
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - James G Elkins
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
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Taillefer M, Sparling R. Glycolysis as the Central Core of Fermentation. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2017; 156:55-77. [PMID: 26907549 DOI: 10.1007/10_2015_5003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The increasing concerns of greenhouse gas emissions have increased the interest in dark fermentation as a means of productions for industrial chemicals, especially from renewable cellulosic biomass. However, the metabolism, including glycolysis, of many candidate organisms for cellulosic biomass conversion through consolidated bioprocessing is still poorly understood and the genomes have only recently been sequenced. Because a variety of industrial chemicals are produced directly from sugar metabolism, the careful understanding of glycolysis from a genomic and biochemical point of view is essential in the development of strategies for increasing product yields and therefore increasing industrial potential. The current review discusses the different pathways available for glycolysis along with unexpected variations from traditional models, especially in the utilization of alternate energy intermediates (GTP, pyrophosphate). This reinforces the need for a careful description of interactions between energy metabolites and glycolysis enzymes for understanding carbon and electron flux regulation.
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Affiliation(s)
- M Taillefer
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada, R3T 2N2
| | - R Sparling
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada, R3T 2N2.
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LacI Transcriptional Regulatory Networks in Clostridium thermocellum DSM1313. Appl Environ Microbiol 2017; 83:AEM.02751-16. [PMID: 28003194 DOI: 10.1128/aem.02751-16] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 12/14/2016] [Indexed: 12/30/2022] Open
Abstract
Organisms regulate gene expression in response to the environment to coordinate metabolic reactions. Clostridium thermocellum expresses enzymes for both lignocellulose solubilization and its fermentation to produce ethanol. One LacI regulator termed GlyR3 in C. thermocellum ATCC 27405 was previously identified as a repressor of neighboring genes with repression relieved by laminaribiose (a β-1,3 disaccharide). To better understand the three C. thermocellum LacI regulons, deletion mutants were constructed using the genetically tractable DSM1313 strain. DSM1313 lacI genes Clo1313_2023, Clo1313_0089, and Clo1313_0396 encode homologs of GlyR1, GlyR2, and GlyR3 from strain ATCC 27405, respectively. Growth on cellobiose or pretreated switchgrass was unaffected by any of the gene deletions under controlled-pH fermentations. Global gene expression patterns from time course analyses identified glycoside hydrolase genes encoding hemicellulases, including cellulosomal enzymes, that were highly upregulated (5- to 100-fold) in the absence of each LacI regulator, suggesting that these were repressed under wild-type conditions and that relatively few genes were controlled by each regulator under the conditions tested. Clo1313_2022, encoding lichenase enzyme LicB, was derepressed in a ΔglyR1 strain. Higher expression of Clo1313_1398, which encodes the Man5A mannanase, was observed in a ΔglyR2 strain, and α-mannobiose was identified as a probable inducer for GlyR2-regulated genes. For the ΔglyR3 strain, upregulation of the two genes adjacent to glyR3 in the celC-glyR3-licA operon was consistent with earlier studies. Electrophoretic mobility shift assays have confirmed LacI transcription factor binding to specific regions of gene promoters.IMPORTANCE Understanding C. thermocellum gene regulation is of importance for improved fundamental knowledge of this industrially relevant bacterium. Most LacI transcription factors regulate local genomic regions; however, a small number of those genes encode global regulatory proteins with extensive regulons. This study indicates that there are small specific C. thermocellum LacI regulons. The identification of LacI repressor activity for hemicellulase gene expression is a key result of this work and will add to the small body of existing literature on the area of gene regulation in C. thermocellum.
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Artzi L, Bayer EA, Moraïs S. Cellulosomes: bacterial nanomachines for dismantling plant polysaccharides. Nat Rev Microbiol 2017; 15:83-95. [PMID: 27941816 DOI: 10.1038/nrmicro.2016.164] [Citation(s) in RCA: 235] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cellulosomes are multienzyme complexes that are produced by anaerobic cellulolytic bacteria for the degradation of lignocellulosic biomass. They comprise a complex of scaffoldin, which is the structural subunit, and various enzymatic subunits. The intersubunit interactions in these multienzyme complexes are mediated by cohesin and dockerin modules. Cellulosome-producing bacteria have been isolated from a large variety of environments, which reflects their prevalence and the importance of this microbial enzymatic strategy. In a given species, cellulosomes exhibit intrinsic heterogeneity, and between species there is a broad diversity in the composition and configuration of cellulosomes. With the development of modern technologies, such as genomics and proteomics, the full protein content of cellulosomes and their expression levels can now be assessed and the regulatory mechanisms identified. Owing to their highly efficient organization and hydrolytic activity, cellulosomes hold immense potential for application in the degradation of biomass and are the focus of much effort to engineer an ideal microorganism for the conversion of lignocellulose to valuable products, such as biofuels.
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Affiliation(s)
- Lior Artzi
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 234 Herzl Street, Rehovot 7610001, Israel
| | - Edward A Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 234 Herzl Street, Rehovot 7610001, Israel
| | - Sarah Moraïs
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 234 Herzl Street, Rehovot 7610001, Israel
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Poudel S, Giannone RJ, Rodriguez M, Raman B, Martin MZ, Engle NL, Mielenz JR, Nookaew I, Brown SD, Tschaplinski TJ, Ussery D, Hettich RL. Integrated omics analyses reveal the details of metabolic adaptation of Clostridium thermocellum to lignocellulose-derived growth inhibitors released during the deconstruction of switchgrass. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:14. [PMID: 28077967 PMCID: PMC5223564 DOI: 10.1186/s13068-016-0697-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 12/24/2016] [Indexed: 05/03/2023]
Abstract
BACKGROUND Clostridium thermocellum is capable of solubilizing and converting lignocellulosic biomass into ethanol. Although much of the work-to-date has centered on characterizing this microbe's growth on model cellulosic substrates, such as cellobiose, Avicel, or filter paper, it is vitally important to understand its metabolism on more complex, lignocellulosic substrates to identify relevant industrial bottlenecks that could undermine efficient biofuel production. To this end, we have examined a time course progression of C. thermocellum grown on switchgrass to assess the metabolic and protein changes that occur during the conversion of plant biomass to ethanol. RESULTS The most striking feature of the metabolome was the observed accumulation of long-chain, branched fatty acids over time, implying an adaptive restructuring of C. thermocellum's cellular membrane as the culture progresses. This is undoubtedly a response to the gradual accumulation of lignocellulose-derived inhibitory compounds as the organism deconstructs the switchgrass to access the embedded cellulose. Corroborating the metabolomics data, proteomic analysis revealed a corresponding time-dependent increase in various enzymes, including those involved in the interconversion of branched amino acids valine, leucine, and isoleucine to iso- and anteiso-fatty acid precursors. Additionally, the metabolic accumulation of hemicellulose-derived sugars and sugar alcohols concomitant with increased abundance of enzymes involved in C5 sugar metabolism/pentose phosphate pathway indicates that C. thermocellum shifts glycolytic intermediates to alternate pathways to modulate overall carbon flux in response to C5 sugar metabolites that increase during lignocellulose deconstruction. CONCLUSIONS Integrated omic platforms provided complementary systems biological information that highlight C. thermocellum's specific response to cytotoxic inhibitors released during the deconstruction and utilization of switchgrass. These additional viewpoints allowed us to fully realize the level to which the organism adapts to an increasingly challenging culture environment-information that will prove critical to C. thermocellum's industrial efficacy.
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Affiliation(s)
- Suresh Poudel
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37831 USA
- Department of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996 USA
| | | | - Miguel Rodriguez
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37831 USA
| | - Babu Raman
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37831 USA
- Dow AgroSciences, 9330 Zionsville Road, Indianapolis, IN 46268 USA
| | - Madhavi Z. Martin
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37831 USA
| | - Nancy L. Engle
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37831 USA
| | | | - Intawat Nookaew
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37831 USA
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR 72205 USA
| | - Steven D. Brown
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37831 USA
- Department of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996 USA
| | | | - David Ussery
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37831 USA
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR 72205 USA
| | - Robert L. Hettich
- Chemical Sciences Division, Oak Ridge National Lab, Oak Ridge, TN 37831 USA
- Department of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996 USA
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Brás JLA, Pinheiro BA, Cameron K, Cuskin F, Viegas A, Najmudin S, Bule P, Pires VMR, Romão MJ, Bayer EA, Spencer HL, Smith S, Gilbert HJ, Alves VD, Carvalho AL, Fontes CMGA. Diverse specificity of cellulosome attachment to the bacterial cell surface. Sci Rep 2016; 6:38292. [PMID: 27924829 PMCID: PMC5141474 DOI: 10.1038/srep38292] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 11/07/2016] [Indexed: 12/02/2022] Open
Abstract
During the course of evolution, the cellulosome, one of Nature's most intricate multi-enzyme complexes, has been continuously fine-tuned to efficiently deconstruct recalcitrant carbohydrates. To facilitate the uptake of released sugars, anaerobic bacteria use highly ordered protein-protein interactions to recruit these nanomachines to the cell surface. Dockerin modules located within a non-catalytic macromolecular scaffold, whose primary role is to assemble cellulosomal enzymatic subunits, bind cohesin modules of cell envelope proteins, thereby anchoring the cellulosome onto the bacterial cell. Here we have elucidated the unique molecular mechanisms used by anaerobic bacteria for cellulosome cellular attachment. The structure and biochemical analysis of five cohesin-dockerin complexes revealed that cell surface dockerins contain two cohesin-binding interfaces, which can present different or identical specificities. In contrast to the current static model, we propose that dockerins utilize multivalent modes of cohesin recognition to recruit cellulosomes to the cell surface, a mechanism that maximises substrate access while facilitating complex assembly.
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Affiliation(s)
- Joana L. A. Brás
- Centro Interdisciplinar de Investigação em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, 1300-477 Lisboa, Portugal
- NZYTech Genes & Enzymes, Campus do Lumiar, Estrada do Paço do Lumiar, Edifício E, r/c, 1649-038 Lisboa, Portugal
| | - Benedita A. Pinheiro
- Centro Interdisciplinar de Investigação em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, 1300-477 Lisboa, Portugal
- UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Kate Cameron
- Centro Interdisciplinar de Investigação em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, 1300-477 Lisboa, Portugal
| | - Fiona Cuskin
- Institute for Cell and Molecular Biosciences, Newcastle University, The Medical School, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Aldino Viegas
- UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
- Institute of Physical Biology, Heinrich Heine University, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Shabir Najmudin
- Centro Interdisciplinar de Investigação em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, 1300-477 Lisboa, Portugal
| | - Pedro Bule
- Centro Interdisciplinar de Investigação em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, 1300-477 Lisboa, Portugal
| | - Virginia M. R. Pires
- Centro Interdisciplinar de Investigação em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, 1300-477 Lisboa, Portugal
| | - Maria João Romão
- UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Edward A. Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Holly L. Spencer
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, ON K7L 3N6, Canada
| | - Steven Smith
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, ON K7L 3N6, Canada
| | - Harry J. Gilbert
- Institute for Cell and Molecular Biosciences, Newcastle University, The Medical School, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Victor D. Alves
- Centro Interdisciplinar de Investigação em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, 1300-477 Lisboa, Portugal
| | - Ana Luísa Carvalho
- UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Carlos M. G. A. Fontes
- Centro Interdisciplinar de Investigação em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, 1300-477 Lisboa, Portugal
- NZYTech Genes & Enzymes, Campus do Lumiar, Estrada do Paço do Lumiar, Edifício E, r/c, 1649-038 Lisboa, Portugal
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Olson DG, Hörl M, Fuhrer T, Cui J, Zhou J, Maloney MI, Amador-Noguez D, Tian L, Sauer U, Lynd LR. Glycolysis without pyruvate kinase in Clostridium thermocellum. Metab Eng 2016; 39:169-180. [PMID: 27914869 DOI: 10.1016/j.ymben.2016.11.011] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 10/21/2016] [Accepted: 11/30/2016] [Indexed: 01/05/2023]
Abstract
The metabolism of Clostridium thermocellum is notable in that it assimilates sugar via the EMP pathway but does not possess a pyruvate kinase enzyme. In the wild type organism, there are three proposed pathways for conversion of phosphoenolpyruvate (PEP) to pyruvate, which differ in their cofactor usage. One path uses pyruvate phosphate dikinase (PPDK), another pathway uses the combined activities of PEP carboxykinase (PEPCK) and oxaloacetate decarboxylase (ODC). Yet another pathway, the malate shunt, uses the combined activities of PEPCK, malate dehydrogenase and malic enzyme. First we showed that there is no flux through the ODC pathway by enzyme assay. Flux through the remaining two pathways (PPDK and malate shunt) was determined by dynamic 13C labeling. In the wild-type strain, the malate shunt accounts for about 33±2% of the flux to pyruvate, with the remainder via the PPDK pathway. Deletion of the ppdk gene resulted in a redirection of all pyruvate flux through the malate shunt. This provides the first direct evidence of the in-vivo function of the malate shunt.
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Affiliation(s)
- Daniel G Olson
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA.
| | - Manuel Hörl
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Tobias Fuhrer
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Jingxuan Cui
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Jilai Zhou
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Marybeth I Maloney
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Daniel Amador-Noguez
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Liang Tian
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Lee R Lynd
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA.
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46
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Advances in Consolidated Bioprocessing Using Clostridium thermocellumand Thermoanaerobacter saccharolyticum. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807796.ch10] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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CO2-fixing one-carbon metabolism in a cellulose-degrading bacterium Clostridium thermocellum. Proc Natl Acad Sci U S A 2016; 113:13180-13185. [PMID: 27794122 DOI: 10.1073/pnas.1605482113] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Clostridium thermocellum can ferment cellulosic biomass to formate and other end products, including CO2 This organism lacks formate dehydrogenase (Fdh), which catalyzes the reduction of CO2 to formate. However, feeding the bacterium 13C-bicarbonate and cellobiose followed by NMR analysis showed the production of 13C-formate in C. thermocellum culture, indicating the presence of an uncharacterized pathway capable of converting CO2 to formate. Combining genomic and experimental data, we demonstrated that the conversion of CO2 to formate serves as a CO2 entry point into the reductive one-carbon (C1) metabolism, and internalizes CO2 via two biochemical reactions: the reversed pyruvate:ferredoxin oxidoreductase (rPFOR), which incorporates CO2 using acetyl-CoA as a substrate and generates pyruvate, and pyruvate-formate lyase (PFL) converting pyruvate to formate and acetyl-CoA. We analyzed the labeling patterns of proteinogenic amino acids in individual deletions of all five putative PFOR mutants and in a PFL deletion mutant. We identified two enzymes acting as rPFOR, confirmed the dual activities of rPFOR and PFL crucial for CO2 uptake, and provided physical evidence of a distinct in vivo "rPFOR-PFL shunt" to reduce CO2 to formate while circumventing the lack of Fdh. Such a pathway precedes CO2 fixation via the reductive C1 metabolic pathway in C. thermocellum These findings demonstrated the metabolic versatility of C. thermocellum, which is thought of as primarily a cellulosic heterotroph but is shown here to be endowed with the ability to fix CO2 as well.
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Thompson RA, Dahal S, Garcia S, Nookaew I, Trinh CT. Exploring complex cellular phenotypes and model-guided strain design with a novel genome-scale metabolic model of Clostridium thermocellum DSM 1313 implementing an adjustable cellulosome. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:194. [PMID: 27602057 PMCID: PMC5012057 DOI: 10.1186/s13068-016-0607-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 08/26/2016] [Indexed: 05/06/2023]
Abstract
BACKGROUND Clostridium thermocellum is a gram-positive thermophile that can directly convert lignocellulosic material into biofuels. The metabolism of C. thermocellum contains many branches and redundancies which limit biofuel production, and typical genetic techniques are time-consuming. Further, the genome sequence of a genetically tractable strain C. thermocellum DSM 1313 has been recently sequenced and annotated. Therefore, developing a comprehensive, predictive, genome-scale metabolic model of DSM 1313 is desired for elucidating its complex phenotypes and facilitating model-guided metabolic engineering. RESULTS We constructed a genome-scale metabolic model iAT601 for DSM 1313 using the KEGG database as a scaffold and an extensive literature review and bioinformatic analysis for model refinement. Next, we used several sets of experimental data to train the model, e.g., estimation of the ATP requirement for growth-associated maintenance (13.5 mmol ATP/g DCW/h) and cellulosome synthesis (57 mmol ATP/g cellulosome/h). Using our tuned model, we investigated the effect of cellodextrin lengths on cell yields, and could predict in silico experimentally observed differences in cell yield based on which cellodextrin species is assimilated. We further employed our tuned model to analyze the experimentally observed differences in fermentation profiles (i.e., the ethanol to acetate ratio) between cellobiose- and cellulose-grown cultures and infer regulatory mechanisms to explain the phenotypic differences. Finally, we used the model to design over 250 genetic modification strategies with the potential to optimize ethanol production, 6155 for hydrogen production, and 28 for isobutanol production. CONCLUSIONS Our developed genome-scale model iAT601 is capable of accurately predicting complex cellular phenotypes under a variety of conditions and serves as a high-quality platform for model-guided strain design and metabolic engineering to produce industrial biofuels and chemicals of interest.
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Affiliation(s)
- R. Adam Thompson
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN 37996 USA
- Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Sanjeev Dahal
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Comparative Genomics Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Sergio Garcia
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Department of Chemical and Biomolecular Engineering, University of Tennessee, 1512 Middle Dr., DO#432, Knoxville, TN 37996 USA
| | - Intawat Nookaew
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Comparative Genomics Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205 USA
| | - Cong T. Trinh
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN 37996 USA
- Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Department of Chemical and Biomolecular Engineering, University of Tennessee, 1512 Middle Dr., DO#432, Knoxville, TN 37996 USA
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Munir RI, Spicer V, Krokhin OV, Shamshurin D, Zhang X, Taillefer M, Blunt W, Cicek N, Sparling R, Levin DB. Transcriptomic and proteomic analyses of core metabolism in Clostridium termitidis CT1112 during growth on α-cellulose, xylan, cellobiose and xylose. BMC Microbiol 2016; 16:91. [PMID: 27215540 PMCID: PMC4877739 DOI: 10.1186/s12866-016-0711-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 05/16/2016] [Indexed: 01/15/2023] Open
Abstract
Background Clostridium termitidis CT1112 is an anaerobic, Gram-positive, mesophilic, spore-forming, cellulolytic bacterium, originally isolated from the gut of a wood feeding termite Nasusitermes lujae. It has the ability to hydrolyze both cellulose and hemicellulose, and ferment the degradation products to acetate, formate, ethanol, lactate, H2, and CO2. It is therefore ges in gene and gene product expression during growth of C. termitidis on cellobiose, xylose, xylan, and α–cellulose. Results Correlation of transcriptome and proteome data with growth and fermentation profiles identified putative carbon-catabolism pathways in C. termitidis. The majority of the proteins associated with central metabolism were detected in high abundance. While major differences were not observed in gene and gene-product expression for enzymes associated with metabolic pathways under the different substrate conditions, xylulokinase and xylose isomerase of the pentose phosphate pathway were found to be highly up-regulated on five carbon sugars compared to hexoses. In addition, genes and gene-products associated with a variety of cellulosome and non-cellulosome associated CAZymes were found to be differentially expressed. Specifically, genes for cellulosomal enzymes and components were highly expressed on α–cellulose, while xylanases and glucosidases were up-regulated on 5 carbon sugars with respect to cellobiose. Chitinase and cellobiophosphorylases were the predominant CAZymes expressed on cellobiose. In addition to growth on xylan, the simultaneous consumption of two important lignocellulose constituents, cellobiose and xylose was also demonstrated. Conclusion There are little changes in core-metabolic pathways under the different carbon sources compared. The most significant differences were found to be associated with the CAZymes, as well as specific up regulation of some key components of the pentose phosphate pathway in the presence of xylose and xylan. This study has enhanced our understanding of the physiology and metabolism of C. termitidis, and provides a foundation for future studies on metabolic engineering to optimize biofuel production from natural biomass. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0711-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Riffat I Munir
- Department of Biosystems Engineering, University of Manitoba, R3T 5N6, Winnipeg, MB, Canada
| | - Victor Spicer
- Department of Physics and Astronomy, University of Manitoba, R3T 5N6, Winnipeg, MB, Canada.,Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, R3T 5N6, Winnipeg, MB, Canada
| | - Oleg V Krokhin
- Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, R3T 5N6, Winnipeg, MB, Canada
| | - Dmitry Shamshurin
- Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, R3T 5N6, Winnipeg, MB, Canada
| | - XiangLi Zhang
- Department of Plant Science, University of Manitoba, R3T 5N6, Winnipeg, MB, Canada
| | - Marcel Taillefer
- Department of Microbiology, University of Manitoba, R3T 5N6, Winnipeg, MB, Canada
| | - Warren Blunt
- Department of Biosystems Engineering, University of Manitoba, R3T 5N6, Winnipeg, MB, Canada
| | - Nazim Cicek
- Department of Biosystems Engineering, University of Manitoba, R3T 5N6, Winnipeg, MB, Canada
| | - Richard Sparling
- Department of Microbiology, University of Manitoba, R3T 5N6, Winnipeg, MB, Canada
| | - David B Levin
- Department of Biosystems Engineering, University of Manitoba, R3T 5N6, Winnipeg, MB, Canada.
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Abstract
Designer cellulosomes consist of chimeric cohesin-bearing scaffoldins for the controlled incorporation of recombinant dockerin-containing enzymes. The largest designer cellulosome reported to date is a chimeric scaffoldin that contains 6 cohesins. This scaffoldin represented a technical limit of sorts, since adding another cohesin proved problematic, owing to resultant low expression levels, instability (cleavage) of the scaffoldin polypeptide, and limited numbers of available cohesin-dockerin specificities—the hallmark of designer cellulosomes. Nevertheless, increasing the number of enzymes integrated into designer cellulosomes is critical, in order to further enhance degradation of plant cell wall material. Adaptor scaffoldins comprise an intermediate type of scaffoldin that can both incorporate various enzymes and attach to an additional scaffoldin. Using this strategy, we constructed an efficient form of adaptor scaffoldin that possesses three type I cohesins for enzyme integration, a single type II dockerin for interaction with an additional scaffoldin, and a carbohydrate-binding module for targeting to the cellulosic substrate. In parallel, we designed a hexavalent scaffoldin capable of connecting to the adaptor scaffoldin by the incorporation of an appropriate type II cohesin. The resultant extended designer cellulosome comprised 8 recombinant enzymes—4 xylanases and 4 cellulases—thereby representing a potent enzymatic cocktail for solubilization of natural lignocellulosic substrates. The contribution of the adaptor scaffoldin clearly demonstrated that proximity between the two scaffoldins and their composite set of enzymes is crucial for optimized degradation. After 72 h of incubation, the performance of the extended designer cellulosome was determined to be approximately 70% compared to that of native cellulosomes. Plant cell wall residues represent a major source of renewable biomass for the production of biofuels such as ethanol via breakdown to soluble sugars. The natural microbial degradation process, however, is inefficient for achieving cost-effective processes in the conversion of plant-derived biomass to biofuels, either from dedicated crops or human-generated cellulosic wastes. The accumulation of the latter is considered a major environmental pollutant. The development of designer cellulosome nanodevices for enhanced plant cell wall degradation thus has major impacts in the fields of environmental pollution, bioenergy production, and biotechnology in general. The findings reported in this article comprise a true breakthrough in our capacity to produce extended designer cellulosomes via synthetic biology means, thus enabling the assembly of higher-order complexes that can supersede the number of enzymes included in a single multienzyme complex.
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